Neon Genesis Evangelion Soul Refrain
by onewingedangel73187
Summary: Shinji is given a Chance to Change the fate of the world. Second Chances are Rare. Rated M for Language, Violence, Sexual Content in later Chaps. Shinji/Rei. *ON HIATUS Until I can get another Computer, and Life levels out, But It WILL continue*
1. Prologue: Ankoku

Shin Seiki EVANGELION: Tamashi no Refuran/ Neon Genesis EVANGELION Soul Refrain

**Refrain**_; _Vulgar Latin _refringere_, and later from Old French _refraindre_ "to repeat",

Prologue: **Ankoku** (Darkness)

Ikari Shinji peeled open his eyelids. As his vision focused, he realized he was no longer in the entry Plug of Evangelion Shogouki. An Orange Sea stretched for endless miles in either direction, he also realized that he was half submerged in said orangish sea and that the nude form of Ayanami Rei was mounted atop him in a VERY peculiar position. Had this poor coward not single handedly caused the destruction of the entire human race, he might have found this erotic, add to the fact his attraction to the blue haired beauty that was atop him. But Shinji had a hard time feeling _anything_ at the moment

'Am I... dead?'

"Ayanami... Where are we?"

"This is the sea of LCL, the sea of the origin of life. This is a world without A.T Fields and therefore without your own shape. You cannot tell the difference between one person or another. An ambiguous world. Everything is yourself, and also not yourself. A dead world."

"I died?"

"Not quite. Everything has combined into one. _This_ is the world you've been hoping for. It is like this."

"But... This isn't it. I don't believe this is it..."

"If you hope that other people exist again, your heart with separate everyone once more. But you will be frightened of other people again."

"It doesn't matter."

The Orangish sea faded away and everything was enveloped in a calm, blue glow.

"Thank you. I feel there are only hateful things there. So running away isn't bad either. But Even of I run way, I can't find a better place. Because the world is without me, now. Just like without everyone else"

A new voice joined them.

"Produce the A.T Field once more... Hurting other people again, that's okay?"

Shinji looked up from his resting place on Rei's lap

"Kaworu-kun?"

Its been a while, Shinji-kun"

"Why are you here, Kaworu-kun?"

" I am your guide, Shinji-kun."

Shinji's confused look spoke for itself.

"What if I told you that no one had to be hurt. That I could give you another chance to right these wrongs? Save everyone; Katsuragi-san, Soryu-san, Suzuhara-kun. Even Rei-chan."

This caught Shinji's attention

"How?"

"How is not important, But whether you desire this chance..."

Shinji was silent. Kaworu sighed, he knew that Shinji did not desire the world to come, but Shinji's nature would paralyze him in this endeavor.

"Come with me, Shinji-kun; I have some things I wish to show you."

Shinji looked to the blue haired albino sitting behind him. She stood and tool his hand in hers, beckoning him to rise with here. Shinji blushed fiercely. Kaworu smiled once, then a serious look settled back on his face. The Endless Blue surrounding them was swept away and replaced with an endless darkness; which also gifted Shinji and Rei with their clothes, which in turn was replaced with a train station, right out of Shinji's memory; the day his father abandoned him. Shinji fixed his eyes on the ground; a hateful fire burning behind his cobalt eyes, and his free hand clenched so tight his knuckles were white and blood trickled through his fingers. Kaworu noticed this, but decided to speak.

"Your situation was a coin toss in this. There were two ways to go from abandonment. It either weakens you and you become cowardly. _Or_ it forges you like an unbreakable sword. Unfortunately, you lost both parents in quick succession, it was enough to break anyone, much less anyone at the age of four."

"I began to think it was my fault. That Father left me because it was my fault Mother died. I pleaded with him to stay, swore I'd be a good boy, but he just walked away. I began to be afraid that any and everyone I loved would die or leave me."

"Yes. That fear began to permeate into other parts of your personality, transforming you into a coward."

The scene returned to the endless blackness, then became the Terminal Dogma. Shinji watched the scene play out as Rei rejected his father in favor of Shinji himself. Shocked he turned his gaze to Rei once more.

"Ayanami, why'd you do that?"

Kaworu let out a knowing chuckle.

"Isn't it obvious, Shinji-kun"

Shinji turned back to Kaworu, a quizzical look crossing his face. Kaworu stared ahead once more as Darkness again settled.

"Many of your friends last thoughts were of you, Shinji-kun. Such as Suzuhara-kun;"

Shinji heard Touji's voice in the pitch black.

"Shinji, I know you can't hear me. But it wasn't your fault that I lost my limbs."

"Aida-kun;"

"Shinji, if anyone can save us, its you."

"Even your father;"

"Father?!"

"Sorry, Shinji"

"You see Shinji-kun, they all believed in your strength. Even your father."

Something inside Shinji snapped.

"Strength?! What strength, do I have?! I'm just a coward who can't do anything right!"

Rei's soft voice filled Shinji's ears.

"That is not true, Ikari-kun"

Shinji turned to face Rei again.

"When the fifth angel attacked, you intentionally caused yourself injury to ensure my safety."

"And When you saw what the fourteenth Angel had done to Rei-chan's EVA, your desires ultimately lead Unit 01 to tear it apart and eat its heart. These two particular instances were caused directly by your desires, Your mother had a hand in dispatching the fourteenth of course."

"But I-"

Kaworu stood in front of Shinji.

"You have the strength..."

Kaworu touched his index and middle fingers over Shinji's heart.

"...Here. You must let go of your weakness."

Shinji stared at the ground, he could feel something strange going on in his chest. He looked at Kaworu and asked the deciding question;

"What happens if I don't"

Kaworu sighed.

"I'll show you."

The darkness faded to become a desolate wasteland, stained red. Rei and Shinji stood beside Kaworu on a cliff overhanging the beach with water the color of blood lapping at the shore. Shinji's eyes widened in horror as he witnessed himself attempting to strangle Asuka.

"You don't succeed this time, but a few days later, Soryu-san mentions Rei-chan in a negative connotation. Well; lets just say it doesn't end well for her. And all alone, swallowed by despair and loneliness, you drown yourself several days later."

Shinji felt if he'd been slapped in the face by the truth.

"I killed Asuka... for Rei?"

"Do you still try to fool yourself otherwise? Your attractions to Soryu-san and Katsuragi-san were superficial at best, that is not to say that you did not care for them in your own way, and they you. However, you and Rei-chan have a bond, that neither of you realized or would allow yourselves to admit. Now Shinji-kun, does everyone, Rei-chan included, die, or do you set the world as it should have been?"

"But How?! How Am I supposed to save the world?! When the sixteenth angel attacked I couldn't...I couldn't even save...Rei."

Tears streaked down Shinji's cheeks as he collapsed to his knees. Tears began to collect on the ground.

"You can change that Ikari-kun."

Rei knelt beside Shinji as Kaworu continued.

"The first step of every Journey takes incredible courage. You have it in you, Shinji-kun"

Shinji stared at the stained earth, his mind racing. Did he truly love Rei? He liked her, but did he **love** her? Would he die for her? The deeper he looked within himself he found the answer blatantly obvious. All of the times he thought of her, the little interactions between them, a small smile, a quiet thank you, the indescribable pain; when she and EVA 00 exploded; that robbed him of his tears, right down to the battle with Ramiel, when he blindly rushed in to pry the hatch off of the severely damaged EVA 00 entry plug. He'd be willing to give his life so Rei could live. And she would do, and had done, the same for him. Shinji stroked Rei's cheek with his right hand.

Such close contact. It was Shinji's deepest desire, and his biggest fear.

Yet as the final tear fell, Shinji realized that he wasn't afraid anymore. For the first time in his life Shinji's heart was filled with unbelievable strength.

Kaworu smiled.

'He is ready.'

"Its not as hard as it seems, is it, Shinji-kun?."

Shinji stood once more and looked to Kaworu.

"What did you do to me?"

"I just gave you a push in the right direction. Whether you stay on that path is up to you."

"If I go back, I can save everyone; Rei? Misato? Asuka? My Father?"

"Yes."

"Will I still have my memories?"

"Yes."

"Then the choice is simple; There is **no** choice. I won't watch them die again. I'm tired of running. I mustn't run away. I can't run away. I **won't** run away."

"Then it is settled. We will send you back to the day it began. Humanity is in your hands, Shinji-kun."

Shinji-began to feel himself drift away; literally pulled away from the ground, Rei and Kaworu smiling after him

"Good bye, Shinji-kun, maybe this time we can love each other like we were meant to."

"Hey, Shinji-kun, I almost forgot to tell you; You're welcome for the gifts, Good bye; brother!"

As his vision whited out, Shinji was allowed a final thought;

'What gifts?'

* * *

Shinji blinked once and found himself holding the green reciever of a payphone. He slammed the phone down, Ikari Shinji's soul burning with a fire he had never known before. He knew what he had to do. He had his own scenario, and he would do it right this time.

"I have to, for you, Rei"

Continued...


	2. Ep 1 Saisei

Shin Seiki EVANGELION: Tamashi no Refuran/ Neon Genesis EVANGELION: Soul Refrain

Episode 1- Saisei(Rebirth)

Shinji peered about, he could hear the aircraft approaching in the background, no doubt engaged in battle with Sachiel, the third Angel. Remembering that an incredibly loud sonic boom was about to echo through the air, Shinji quickly threw his hands over his ears. It didn't help much, but it was better than nothing.

"Why the hell isn't Misato here yet?!"

Shinji looked to the air to see the UN VTOLs futilely engaging Sachiel.

"Damn, that thing is still so ugly."

After a useless Hail of missiles Sachiel swatted one of the VTOLs out of the air, the wreckage nearly crushing Shinji.

"Of all the things I should have remembered, I didn't remember that."

Luckily he knew that it meant that Misato's arrival was imminent. Even as the Angel of Water landed on the wreckage, causing a minor explosion, Misato's car screeched to a halt.

"Sorry for keeping you waiting!"

Shinji nodded and scrambled into the car. When they were a safe difference away from the combat zone, Misato pulled over and pulled out a pair of binoculars. Shinji remembered the last time; Misato had thrown herself over him to protect him for the blast of the incoming N^2 mine. Shinji decided to return the favor.

"Wait... Don't tell me they're going to use an N^2 mine?!"

"GET DOWN!" Shinji threw himself to cover her. The shock wave flipped the blue Renault Alpine on its side. t occupants poked their heads out and stared at the mushroom cloud.

When the sky returned to normal, Shinji leapt from the car, Misato climbing out after him, falling flat on her ass. Shinji extended a hand to her.

"Are you alright, Katsuragi-san?"

Misato accepted the hand and Shinji lifted her to her feet making her blush and giving her a weird feeling of deja vu.

"Misato is fine... You know, I feel like we've known each other for a long time..."

Shinji smiled at the notion.

"Perhaps we knew each other in a past life."

'Which is technically true. So far so good... I'll try to stick as close to the original as I can, for now.'

Shinji looked over to the flipped car, before proceeding to attempt flipping the vehicle back on its wheels. Misato jumped up immediately and assisted the young boy. After a good two or three shoves the Alpine landed back on its wheels with a thud.

"Thank you, Shinji-kun."

Misato looked at her car.

"What a mess... I don't think it'll get us back to headquarters."

"Will these do the trick, Misato-san?"

While Misato had been grieving the damage to her car, Shinji had walked to the nearby shop and grabbed the batteries as Misato had in the original time line.

"Yeah! You're pretty innovative."

Shinji blushed slightly as he helped the violet haired woman connect the batteries to her car.

***

Within Minutes they were zooming toward NERV HQ. Shinji heard Misato requesting a direct train line to HQ, and ensuring his own safe arrival. After getting off the phone, Shinji could swear she was holding an internal monologue.

"Misato-san? They won't mind if we use these will they?"

"Of course they won't Besides I'm an international government agent."

Shinji laughed remembering the first time this happened. But like a few other minor details so far, Shinji decided to go a different path.

" I suppose that's true."

'Phew, at least she didn't fishtail the car this time...'

Within a half hour they had finally arrived at the track where the train would take them to the Geofront, and the True beginning of Shinji's own scenario.

'Probably best to act like I don't know what's going on...'

"Special Duty Organization NERV?"

Shinji's question referred to the insignia of NERV emblazoned on the bulkhead of the railway.

"Its a secret organization under the control of the United Nations."

"That's where Father is, right?"

Ikari Gendou's menacing figure flashed through the younger Ikari's mind.

"Well yea. Do you know what he does?"

"My teacher told me his work is vital for the protection of the human race. So, you're taking me to Father."

"Pretty much."

A few minutes of silence passed. In the Original Timeline, Shinji had been gripped with Apprehension. This time his silence was meditative, as he prepared the first act to commence. Not to say he still wasn't nervous

"That reminds me, Did you get an ID from your father?"

"Yeah."

Shinji dug the slip of paper out of his briefcase and presented to Misato.

"Here it is."

"Thanks."

Misato took the piece of paper and inspected it. She handed him a book.

"Then read this."

Shinji accepted the NERV Orientation Booklet. Though he knew its contents by heart, he feigned reading it anyway.

"Am I going to work for them too?"

Misato was silent. Shinji continued

"Of course, he wouldn't have sent me a letter unless he needed me for something."

"I see, so you don't get along with your father, I was the same way."

A moment later the tunnel opened into the Geofront, still beautiful, and Shinji once again feigned ignorance.

"Wow a real Geofront!"

"Yes, this is our Secret base; NERV HQ, the key to rebuilding our world and a fortress for all mankind.

***

Rather than suffer Misato's lack of direction, Shinji immediately asked to see the interior map.

Where are we going?"

Of course Shinji knew exactly where. But acted like he was looking to make sure the directions were right. When they reached the elevator, they bumped into Ritsuko, whom was actually on her way to whatever it was she had been doing in the original time line.

"Misato? You actually didn't get lost?!"

"All thanks to Shinji-kun here. His first time here and he can read that damn map better than me."

"So this is him?"

"Yes, I'm Ikari Shinji. I am honored to meet you Akagi-hakase."

"The Third Children according to the Marduk Report."

"He's quite unlike his father."

'And to think, last time they said you were just like him. You must be doing something right, Ikari.'

"Well I suppose my diving will have to wait."

As if to answer Ritsuko's statement, the P.A began issuing an order to assume battle stations level one.

While Misato discussed the upcoming confrontation and the odds of EVA Unit 01's Activation. Shinji was preparing to put on the biggest act of his young life.

***

They entered the pitch black holding bay for EVA Unit 01.

"Its completely dark in here."

The lights activated on cue. And thus the act began.

Feigning shock, Shinji jumped at the sight of EVA 01.

"A face?! A giant robot?!"

Shinji flipped through the manual, acting like he had the first time he was standing before EVA 01. Once again on cue, Ritsuko spoke.

"You won't find this in the manual. This is mankind's ultimate multipurpose Decisive Weapon; Synthetic Human EVANGELION: Unit-01. Built in absolute secrecy, its mankind's trump card.

"Is this part of what my father's been doing?"

"Correct."

The booming voice that had once intimidated Shinji echoed from above.

"Its been a while."

"Father..."

As he feigned fear, Shinji saw his father smirk.

"We're moving out!"

Misato was shocked by the commander's order.

"Moving out?! Unit 00 is still in cryo-stasis, isn't it?"

Misato glanced over at EVA Shogouki and realized the game plan.

"You're not planning to use Shogouki?!"

"There's No other way."

Ritsuko's response only seemed to make Misato even more debative.

"Hold on! Rei can't do it yet, can she? We've got no pilot!"

"One has just been delivered."

"Are you serious?"

Ritsuko turned her attention to Shinji.

"Ikari Shinji."

"Yes?"

"You will pilot it."

Misato interjected quickly.

"But even Ayanami Rei took seven months to synch with her EVA. Its impossible for him to do it, he just Got here!"

"He just has to sit in the seat. We don't expect more than that."

"But..."

"Repelling that Angle is our ultimate priority. To do that we have no choice but to put aboard the EVA whomever has the chance to synchronize with it, no matter how slight. I believe you know that, Captain Katsuragi."

"I suppose..."

Now that Misato and Ritsuko were done bickering, Shinji once again spoke.

"Father, why did you send for me?"

"You know exactly why."

"So you want me to take THIS thing and fight THAT thing?"

"That's right."

"No way. Why now, I thought you didn't need me!"

"I called you because I have a need for you"

"Why?"

"Because no one else can."

"I can't... I've never seen anything like this before! I can't do this!"

'Okay, so I just lied my ass off.'

"You will be instructed."

"But there's no way I can do this! I can't pilot it!"

"If you're going to pilot do it now, and quickly, if not, Leave!"

Everyone stared at him as the hanger began rumbling from the angel's rampage above. Staring upward, Gendou commented aloud.

"It must have detected our location."

Ritsuko, not knowing Shinji's act, pleaded with him once more.

"Shinji-kun, we don't have the time.

Now it was Misato's turn.

"Get into it."

'Thanks a lot, Misato-san...traitor.'

"No! I didn't come for this! It isn't fair!"

"Why exactly did you come, Shinji-kun? You mustn't run! Not from your father, and most of all, not from yourself."

"I know that! But there's no way I can do it!"

High above the Third Children, Shinji heard his father give the order to wake the First Children, and bring her to the hanger to pilot Shogouki. Ritsuko in turn ordered the system to be reconfigured to the First Children and prepped for reactivation. The Tech team complied.

'Its go time.'

Shinji's ears picked up the sound of the gurney wheels and foot steps before they even brought Rei into the hanger. Shinji watched as they pulled her by him, eyes meeting for but a moment. Rei struggled to sit up, and the sight of her in pain almost made Shinji rethink his strategy, but he held. Sachiel's next blast shook the hanger so hard that Rei's gurney toppled over. Had anyone paid close attention to Shinji's feet, they'd have seen him begin his sprint before the gurney began to tip. Shinji caught Rei in his Arms, and Unit 01's Arm moved to protect Shinji from the falling debris. Amongst the commotion, Shinji whispered something into Rei's ear

"Rest now, I'll protect you."

Shinji glared up at his father, Rei still in his arms.

"You have a pilot father! I'll do it!"

Shinji used his leg to right the gurney before placing Rei upon it. Rei opened her good eye and could hazily make out the form of her savior.

As Soon as Shinji climbed into the entry plug, the activations checklist was run through. As LCL filled the plug, Shinji closed his eyes and steeled his nerves for battle. He wasn't looking forward to this, but he was the only one who could defeat the Angel.

'Let's do this, mother.'

***

Back in the Central Dogma, Ibuki Maya received a shock as Shinji synched with his EVA.

"Amazing, Sempai, His synch ratio is hold at an even 85%!"

"There must be an Error"

"Negative, everything checks out!"

"Its almost as if he's done this before."

Misato's voice echoed through the Central Dogma

"Prepare for Launch!"

All around Shinji, Locks and braces were moving away from his EVA, and it was being moved to the ejector pad.

"Launch path is clear. All systems; Green."

Even as the EVA rocketed up ward, Shinji maintained his calm. Only when he reached the surface of Tokyo-3 did Shinji open his eyes; looking square at Sachiel.

"Are you ready, Shinji-kun?"

"Yeah."

"Release safety locks! EVA Unit 01, Lift off!"

Ritsuko's voice replaced Misato's on the comm.

"Shinji-kun, just concentrate on walking right now."

'Oh Ritsuko-san, I'll do more than walk."

EVA 01 leapt into the air, flipping in mid-air to land heel first in what appeared to be Sachiel's face, propelling the Third Angel backward."

"I need to finish you quick."

Sachiel lunged for EVA 01's arms which Shinji deftly avoided, remembering all too well his first run in with the Angel of Water. Instead Shinji grabbed Sachiel and began to pull its arms in opposite directions before head butting the beast. Sachiel made several more attempts to grapple EVA 01, which earned it several punches to the face.

"Not this time, Motherfucker!"

Within NERV HQ, everyone form Gendou and Fuyutsuki, to Misato and Ritsuko watched in silent awe, every mouth on the bridge hanging open. Shinji booted the angel a clear hundred yards. EVA 01 charged at Sachiel only to collide with its A.T. Field. Shinji chuckled spreading his own A.T. Field and using it to tear through his opponent's A.T. Field.

"It's neutralizing the phase space."

"No, its eroding it!"

"It's over."

"Yes, it seems so."

EVA 01 hoisted Sachiel and German Suplexed it into the street. The EVA followed the attack with a punt to the Angel's core, followed by several successive kicks. Shinji picked the beast up and began hammering the EVA's fists into Sachiel's core. Cracks began to for all over the red orb. Shinji backed the EVA up for a moment, unfortunately this gave the Angel time to maneuver, and it went for the EVA's arms. Shinji countered immediately grabbing both the Angel's arms in one hand, and with an effortless twist of the wrist, snapped them like twigs. EVA 01 deployed its Progressive Knife from its right shoulder pylon. Shinji grabbed the Angel by what appeared to be eye sockets and forced it against a building. Fir the next several seconds the prog knife was driven into the Angel's Core over and over, sparks flying as Shinji drove the blade in once more and twisted it sideways as if to drive the point home. A Fierce Red light began to glow from Sachiel's core. Misato panicked

"Its going to use the last of its energy to self-destruct?!"

"Oh no you don't!"

Shinji pulled the Prog-knife free of Sachiel's core, then proceeded to slice the angel in half starting at its crotch, through its core, and all the way through its head. The Angel slid into two halves smearing purple blood all over the building as it slid down. Labored, exhausted breathing from the pilot was the only sound for a minute before anyone spoke. The voice of Aoba Shigeru shattered the silence.

"T-target has gone silent."

Cheers exploded within the Central Dogma. Ritsuko was beyond impressed with the EVA and its pilot.

"He did it! Unbelievable! What skill!"

Despite everyone's excited chatter, Misato's concern was for the young pilot.

"Shinji-kun, are you alright?"

Silence once again reigned, broken only by more exhausted breathing.

"I'm fine, Misato-san... I'm just so damn tired..."

On screen Shinji-slumped backward.

"Shinji-kun!"

Inspecting brain wave patterns of the pilot, Ritsuko assured the purple-haired captain.

"Calm down, Captain Katsuragi, he just fell asleep."

***

Shinji awoke in a hospital bed. The same hospital bed he had been in time and time again.

'You know, they should just call this the 'Ikari Room'... Man. I don't think I've ever concentrated on defeating an angel that hard before, I wonder what my synch rate came in at.'

Shini sat up and slipped off the bed. He had been successful in destroying the third Angel, albeit causing a lot more damage than he would have liked. But Sachiel was just the first of many obstacles to come. In three weeks, Shamshel would appear. In that minute amount of time, Shinji had quite a few things to accomplish.

'Damn, this saving the world shit still sucks'

Shinji stopped walking realizing he'd traveled quite a distance from his room. He peered inside the room to his right, and saw a girl with blue hair and alabaster skin.

"Rei."

'Am I ready for this?'

Swallowed the lump that had formed in his throat.

'No, I can't think like that. Kaworu said it was up to me to overcome my demons'

Shinji opened the hospital room door and slipped into the room unnoticed. He had some time before Misato showed up, if his memory served him correctly. The albino girl noticed Shinji enter the room and turned her head enough to see him out of her good eye. He smiled at her as he grabbed a chair nearby and set it beside her bed, on her left side.

"Hello."

"You are Commander Ikari's son, correct?"

"Yep. I am the Third Children, designated pilot of EVANGELION Unit 01; Ikari Shinji. And you are Ayanami Rei, right?"

Rei looked at Shinji a moment, he had a gentle smile on his face.

'Ikari-kun's smile... it makes me feel warm... It is a pleasant feeling, an almost...familiar feeling.'

"Yes. I am the First Children, Ayanami Rei. Ikari-kun, why are you in my hospital room?"

"I wanted to make sure you were alright, you took a pretty nasty tumble, Ayanami."

" I have received no further injuries. Ikari-kun."

"Shinji."

"What?"

"Call me Shinji. Ikari sounds too formal. I hope I can call you Rei."

Rei felt the warmth again.

"That would be acceptable, Ika...Shinji-kun."

Shinji smiled even wider, this might be easier than he had originally thought.

"I'm glad, Rei-san. But if I may ask, why would you climb into Unit 01 in your condition."

"I was ordered to."

Shinji frowned.

"So, you'd kill your self if he ordered you to?"

"Yes."

"What about what you want? Doesn't that matter?"

"I-"

The two were interrupted by a nurse that had come to check up on Rei. Shinji stood up and prepared to leave, but turned to Rei one last time.

"Get better soon, Rei-san. Bandages don't suit pretty girls like you."

Shinji leaned over and kissed Rei's forehead, causing her to blush, before picking up the chair and placing it by the wall, then leaving the room. The nurse turned to Rei.

"Your boyfriend?"

"Boyfriend?"

"You know, someone who cares for you with all his heart, someone who loves you."

The nurse went about checking things as she spoke.

"No. I do not have...a boyfriend."

"Well my advice is to not let that one get away. He's the kind that'll make you happy."

***

Shinji was sitting in the waiting room when Misato finally arrived.

"Are you okay?"

"I'm fine, that fight just really wore me out, that's all."

Misato smiled.

"Well come on"

"Yeah."

***

Misato's Renault Alpine sped away from NERV. Shinji once again had played his part to perfection, he was assigned to live Misato, who was now insisting on a welcoming party. Knowing Misato's penchant for instant ramen with her possibly toxic curry, Shinji, volunteered to cook.

"Do you mind if we make a small detour?"

"Where?"

"Some place really cool."

She stopped at the lookout point overlooking most of Tokyo-3. No matter how many times Shinji saw this place, it was always beautiful. As the buildings rose out from the ground Shinji said only one word;

"Beautiful"

"You can say that again, Shinji-kun. This is our city, New Tokyo-3. Its the city you saved."

"Hai."

'And I'll save it again.'

***

Shinji followed behind Misato with a grocery bag in his arms. She unlocked the door and entered, Shinji following. The chaos that was Misato's apartment nearly sent Shinji into cardiac arrest.

'I'd forgotten this hell. No. I blocked it out. Oh man...'

Shinji went about cleaning up Misato's apartment, then preparing dinner. He put a fish and a can of Yebisu down for Penpen, knocking on his fridge to notify the warm water penguin. He set Misato's beer down beside her place at the Table. As he finished up in the kitchen, Shinji heard Misato gasp.

"Shinji-kun... this is... amazing."

"It was the least I could do, Misato-san."

Shinji squatted and patted Penpen on his head, the Penguin squawking happily. Misato watched the scene, once again seized by that feeling of familiarity.

"Let's Eat!"

"Yeah. Let's Eat !"

***

After eating the miniature feast that Shinji had prepared, Shinji cleaned up the table and washed the dishes. It was then that Misato spotted a folded up peice of paper. She opened it up and saw it was a chart of chores. See that she had found his chart Shinji spoke as he dried the dishes.

"I took the liberty of drawing up a chart of chores. That's alright isn't it?"

"But, Shinji-kun, you've taken on so many."

"That's alright, it helps me keep my mind busy."

Shinji finished drying the dishes and putting them away. When he turned around, Misato was right behind him.

"Misato-san?"

Misato didn't reply, instead opting to pull Shinji into a tight hug.

"You sweet, sweet man."

The use of the term man hadn't been lost on the young Ikari. He also couldn't help blushing as Misato practically smothered him with her breasts.

"Misato-san...Can't breathe..."

When Misato released him from her death grip of a hug. Shinji inhaled a deep breath. While death by breast would have been a great way to go, Shinji had opted to continue living, and take care of his critical mission.

"Sorry about that, Shinji-kun. I know! Why don't you take a bath and relax. Everything in the last couple of days must have really worn you out."

"Yeah. that sounds like a good idea."

As Shinji headed toward the bathroom, it didn't even occur to the NERV Operations Director to ask how Shinji knew that Penpen liked Yebisu and fish.

***

Shinji soaked in the bath, the warm water massaging away his stress. Staring up at the ceiling, Shinji found himself lost in thought. He rolled the changes in his personality around in his head, trying to figure out the cause. Then his thoughts drifted to Ayanami Rei.

'Rei. I won't let Father treat you like a puppet this time. You deserve so much better. Even if it kills me, I'll protect you.'

Shinji got out of the tub and dried himself off as the water drained. A soft knock on the door alerted him. Wrapping the towel around his waist, Shinji slid the door open expecting the warm water penguin, but was instead face to face with the busty ops director wearing naught but a green towel.

"Mi-mi-mi-Misato-san!"

'Oh man! What the hell's going on here?! Pull yourself together Ikari! She wouldn't try anything...would she?!'

Giggling slightly at Shinji's beet red face and panicked expression, Misato ruffled the teen's hair.

"You did a very praiseworthy thing today."

Visibly calming, Shinji replied.

"I did what I had to do. If I didn't do it, Father would have made her do it, even in the condition she was in."

"Ritsuko's right, you and your father are practically different species."

Shinji nodded. Still aware of both of their lack of clothing, Shinji decided he'd best move to his room, lest he get flustered once again.

"I'm going to bed now, Misato-san"

"Alright, Shinji-kun, see you in the morning."

Shinji walked past Misato and was halfway down the hall when an idea struck him.

"Misato-san, if you have some free time, Could you...teach me how to swim?"

Misato stared at him a moment, then smiled.

"Sure thing. Shinji-kun, I have some time off coming."

"Arigatou, Misato-san."

With that out of the way, Shinji continue to his room.

***

"You should have seen him Ritsuko! He cleaned the entire place, he's an amazing cook, and he took most of the chores on himself! I tell ya, I think I'm in love."

"Oh come on now, Misato. He's only fourteen."

"I know! I Know! Geez, can't you take a joke?!"

"Ah, shut up. Anyway, get this; he asked me to teach him how to swim, isn't that the sweetest thing?"

"It did mention in his profile that he did not knwo how to swim. But, hai, that is touching."

Misato shifted her position in the tub slightly.

"Well, Misato, I have a lot of work tonight. So I'll talk to you later."

"Alright, talk to ya later, Ritchan."

After hanging up the phone, Misato sat in the tub a while longer, thinking to herself.

'Not that I'd tell Ritsuko, but something feels right about that kid, like I couldn't imagine him not being here... Penpen warmed up to him right away too. Ah maybe I'm thinking too much on this.'

***

Shinji lie in bed staring at the cieling. Once upon a time, he had laid here, and was haunted by his first battle. Now, unfortunately, a seasoned veteran who remembered every strategy used to defeat the Angels, Shinji just stared at the ceiling, mulling over his "scenario." He would have been fifteen soon, But such things were irrelevant, he had a mission to fulfill.

'I will defeat the Angels and save Rei without fail.'

Shinji settled into sleep still contemplating his scenario.

Little did Shinji know, a certain EVA pilot was thinking about him across the city; in the NERV infirmary.

***

The Third Children had been so kind to her, even though they had just met. She wished to learn more about this boy.

'Ikari Shinji-kun... You...intrigue me. I wish to learn more about you. Why do I feel... comfortable, around you, yet uncomfortable when you are not here. Also, this feeling of familiarity; why does it grip me so? What should I do?'

Rei closed her eyes and saw a partial image in the depths of her mind. She heard but one phrase;

"You can just smile."

Continued...

* * *

Next Chapter- Shinji starts school! (Again) Touji beats him up. (Again.) Shamshel attacks (AGAIN! Jesus Christ! Do I see a pattern here or what?!) But before that, dreams haunt the First and Third Children and NERV Ops. Director. Gendou goes "WTF, mate" about Shinji's mysterious personality shift. Shinji plots and Rei wants to learn more about him.

Next Chapter- Yume (Dream)

* * *

A/N: WooT! Author's note Time!

So, who liked Shinji going to town on Sachiel? I DID! And yes I know there is ooc abound in this chapter, its gonna get worse as this goes on, so if you don't like it, you have fair warning.

And addressing the problem with Asuka that one of my reviewers brought up, I do have something special planned for her in the rough drafts, but I am curious of your opinions, barring Shinji and Rei, who would you pair Asuka with?

Anyway, I hope you all enjoy this and I'm already typing up Chapter 2!

Sayonara!

* * *

EDIT 1

Well this has gotten a bunch of reviews only a few days after getting put up. I did take a lot of what was said into consideration and edited the first two chapters accordingly, hopefully it clears up the misunderstanding that I am trying to rush things. Also any advice from veteran NGE fanfic writers is greatly appreciated, as this is my first NGE fic I've posted, and we all know what kind of mind-trip that show is. lol.

EDIT 2-

Due to the fact that two people in particular are complaining about the Japanese in this story, I am henceforth removing the "offending" material, with a full English reference to the EVA units, etc. I will keep the honorifics, however and the Japanese way of Family name before personal are you Happy, Starfire99?


	3. Ep 2 Yume

Shin Seiki EVANGELION: Tamashi no Refuran/ Neon Genesis EVANGELION: Soul Refrain

Episode 2- **Yume** (Dream)

The Top of NERV HQ Exploded as EVA-01 rose from within as if it were an angel from the bowels of Hell. It's A.T Field had become a distinct set of wings. In confusion Shinji quickly glanced around him, fear seizing him as he realized where and when he was. He slowly looked downward, fully expecting to see the mangled remains of EVA-02, but instead bore witness to a sight that made his heart stop and his blood run cold. Below him were the barely recognizable ruins of EVA-00. His breathing became shallow for a moment before a scream that would rival a banshee's erupted from his throat.

***

Shinji's eyes flew open as he bolted upright, breathing in deep labored breaths and plastered in cold sweat.

"What the fuck kind of twisted dream was that?!"

Grabbing his clock, Shinji checked the time; 04:30. Damning his inability to go back to sleep, Shinji stood up, made his bed and decided to take a walk to try and clear his head. Shuffling through his meager selection of clothes, Shinji found himself irritated at his sheer lack of clothing, much less good clothing.

'Note to Self; Get some decent clothing.'

Settling on a black pair of pants and a black t-shirt, Shinji dressed and grabbed his NERV I.D and spare card key for the apartment. While he planned on being back before Misato awoke, he nonetheless quickly scribbled a note explaining where he was and placed it on the table in case she woke up early, however unlikely that was. Double checking to make sure he had what he needed Shinji headed out the door to begin his pre-dawn stroll.

The pre-sunrise air was cool against his skin as Shinji walked around the block, trying to sort out his thoughts. After some time he came to a bridge near where he had battled Sachiel. Observing the damage, Shinji realized he might have been too aggressive, causing much more damage than he had planned. He had seen Search and Rescue crews in the battle zone some days ago, which spoke of injured, Shinji reflected sadly.

"Even with good intentions I'm still getting innocent people hurt."

Shinji slammed his fist down on the railing in frustration

***

Katsuragi Misato broke her kiss with the fourteen year old boy.

"That's an adult kiss, we can finish the rest later…"

She shoved the boy into the elevator and sent it downward before collapsing against the wall. Blood was pouring out of the wound on her back, smearing on the wall as she slid down to the floor.

Then the Floor exploded around her.

***

Misato bolted upright, sweat clinging to her skin and breathing erratically. She checked herself to make sure she wasn't still sleeping or worse…

"What the hell, that…that felt so real."

Misato looked to her window, it was still dark out.

"There's no way I can go back to sleep now, not after a nightmare like that."

Dragging herself out of bed and to the refrigerator, to grab her morning Yebisu, Misato spotted a neatly folded note on the table.

--

Misato,

I couldn't get back to sleep, so I've gone for a walk. I'll be back before breakfast.

Shinji

--

Misato placed the note down on the counter and cracked open the can of beer, leaning against the fridge

"I wonder if he does this sort of thing all of the time?"

***

Shinj was deep in his thoughts, even as he headed back to Misato's apartment.

His major concern for now was the next angel and destroying the core so that it couldn't be salvaged into EVA-04, which would lead to the infestation of EVA-03 by the thirteenth angel.

And though Shinji knew he had a few weeks before the fourth angel made its appearance, he still wanted to be prepared. In his hand was a bag with half a dozen notebooks in which he could compile information, strategies and ideas.

'I'm gonna need help finding out what father is planning, but whom? Kaji won't be here for some time, and Misato and Ritsuko are too risky, just yet. Who does that leave?'

Shinji stopped in front of the apartment door, and was pulling out his keycard when the door flew open to reveal Misato, her arms crossed and an angry look on her face. Shinji smiled nervously and fought the impulse to flee.

"Care to tell me where you've been?"

"I- I left a…a… Note! Note, I left a note. I couldn't get back to sleep, so I…I went for a walk."

Misato sighed, she really shouldn't have been angry with him, he had left a note. But something in the back of her head had been nagging her, as if she should have been worried that he would run away. She offered the teen a soft smile.

"Look, I'm sorry I got angry. But next time, just wake me up and tell me where you're going"

Shinji felt his confidence slowly resurface, he should have known, she was only worried about him.

"I'm sorry Misato, I just needed to straighten a few things out in my head"

"Its alright, but you should hurry up and make breakfast, we have to go to HQ in a little bit."

Misato's statement was punctuated by the growling of her stomach. Shinji just smiled and headed inside.

"I'll get to making breakfast right away."

******************A Couple of Days Later, NERV HQ*************************

"Shinji-kun, have you memorized the positions of all the EVA emergence points, emergency power junctions, armament buildings, and recovery zones?"

"Yes, ma'am"

'If I haven't memorized all of those by now, I'm fucked'

Shinji chuckled to himself.

"Then lets continue where we left off yesterday. We'll initiate Induction Mode."

To Shinji's right a five minute countdown began, and in front of him a simulated mock-up of the Third Angel appeared. Shinji willed his EVA to lift its Pallet Rifle.

"Position Target in the center, then switch on."

Shinji did as ordered, eliminating the first sim-angel.

'Let's mix it up a bit.'

On the next target Shinji shot from behind his back, a surprised look appeared on Maya and Ritsuko's faces.

"Is…is he showing off?"

"I…I think so, sempai."

Misato stood behind them, a confident smirk on her face.

"He's still a kid, let him have a little fun. Given how he tore through the last angel, we should trust that he knows when not to fool around in battle, Ritsuko."

Ritsuko sighed, knowing that Misato was right. What she truly wanted to know was how Shinji was so good at what he did.

*************************NERV Infirmary Wing****************************

Rei heard the door open and Commander Ikari Gendou walked in.

"How are you feeling, Rei?"

"I am well, Commander."

"Good. The doctors tell me you will be fit for duty in a week or so."

"I am glad."

Gendou noticed the distant look in the First Children's eyes.

"Is something troubling you, Rei?"

"No, sir."

Rei thought for a moment.

"I met your son yesterday."

This surprised Gendou, he knew eventually the First and Third Children would meet, but Gendou had his son pegged as a coward, Shinji was not the type to seek someone out. He wondered if this should worry him.

'As long as it does not impact The Scenario, it should be of no concern to me.'

"What are your opinions of the Third, Rei?"

Rei was quiet for a minute or so, as if she was trying to phrase her answer in the correct manner.

"He is…nice"

"I see."

A slight frown found its way onto the First Children's face.

"You are displeased?"

"No, no, its quite alright. It is beneficial to learn about your fellow pilot, keep me informed of these meetings."

"I understand."

Nodding, Gendou turned to leave. Just outside the door, he nearly collided with his son. However unlike the last time, Shinji showed no signs of cowardice. Gendou began to get the uneasy feeling that his son knew something, but shook it off. Very few were privvy to The Scenario, and there was no way his son had any information about it, especially not in the short time he had been in NERV.

"Hello, father."

The two Ikaris stood no more than a foot apart, matching looks of stone set into both faces. Gendou turned to leave, Shinji remaining in place, but followed the Commander with his eyes. Once his father had turned the corner, Shinji sighed and opened the door to Rei's room.

"Hey, Rei-san."

"Hello, Shinji-kun"

"How are you feeling, today?"

"I am well."

Shinji smiled genuinely, before grabbing the chair by the wall once again, sitting beside Rei's bed.

"The doctors have informed the Commander that I will be functional enough to resume my duties with optimal efficiency in one weeks time."

"Rei-san, that's great news."

"Why?"

His excitement of learning about her release from the Infirmary struck Rei as curious.

"Well, because you won't be in this cramped room anymore."

"I see."

'His concern is for me, not my duties as a pilot.'

A blush once again settled on Rei's cheeks.

"You had a harmonics test today, were the result satisfactory?"

'Is Rei… Is she trying to make small talk?'

"Yeah, Ritsuko-san said I did alright"

'Alright is an affirmative answer, but why does he not take pride in this?'

"You are not satisfied with the results?"

"Its not that, the results I got were more than enough to make a few people happy."

'And one German red-head exceedingly jealous.'

"Yet you are not pleased. Why?"

"I don't pilot Unit 01 for myself or some results on a test. I put myself on the line, so others are safe."

'So our reasons for piloting EVA are not dissimilar.'

"So it is a bond then?"

"Something Like that."

"I am also bonded."

Shinji chuckled, the conversation they were having was similar to the one they had in the original timeline before fighting Ramiel.

"We're not so different, Rei-san."

This left Rei speechless, so she did the only thing that came to mind; she smiled.

************************NERV Commander's Office*************************

Gendou sat at his desk observing the interaction between the First and Third Children on a monitor.

'Did she just 'smile' for him?'

Fuyutsuki Kouzou noticed that his former pupil was looking quite perturbed.

"Is something wrong, Ikari?"

"There are glaring errors in the Marduk Organization's profile of the Third Children. The report details the Third Children as a coward who avoids contact as often as possible and from my own past experiences this should prove correct, sensei"

"And?"

"Since his arrival, the Third Children has contradicted these reports, these reports are never in error."

"His actions before, in the EVA cages, did seem like an act. But if this does not affect The Scenario, I hardly see the relevance. Children Grow up, some faster than others, perhaps we should refine the system."

"I hope you're right, sensei."

'What do you know, son?'

***********************NERV Infirmary Wing******************************

Shinji sneezed.

He checked his watch; it read 17:30. Shinji sighed, time had flown by quickly and as much as Shinji wanted to stay he had to get back to Misato's place.

"You are leaving?"

"I'm afraid I have to."

"You fear to leave?"

Shinji chuckled.

"Its an expression, Rei-san. I'll be back to see you again."

***

The drive from NERV was relatively silent, save for the pitter patter of rain against the window. Shinji saw a worried look on Misato's face.

"Is something wrong, Misato?"

"Its nothing to worry about, Shinji-kun, I had a disturbing dream last night."

"Wanna talk about it?"

"Not really, its something I have to sort out for myself.

"I understand."

Once again silence reigned inside of the Renault Alpine.

"Misato-san, have you ever had a dream that felt so real it was like a memory?"

Misato slammed on the brakes, and turned to Shinji with a shocked look on her face.

"H-how did you know?"

Shinji was slightly confused, he had been thinking of his own nightmare.

"Huh?"

Misato swallowed the lump that had formed in her throat.

"My dream last night, it was about…my death. Only it felt less like a dream and more of a hazy memory."

This revelation shocked Shinji, as was written in his eyes.

'Calm down, Ikari, its probably just coincidence. Besides, how could she possibly know, I'm the only one who retained their memories of that original timeline…right?'

He felt the pang of his old self-doubt, but shook it off.

"I can see how that'd be disturbing, Misato-san. Its not everyday someone dreams of their death."

"Yeah…"

Misato put the car back in drive, and they continued on their way. They had made plans to do some shopping, for when Shinji transferred into Tokyo-3 Junior High in two weeks time.

******************************A Few Hours Later**************************

Shinji lie in bed, staring at the ceiling. Aside from the general school supplies, Shinji had also bought some new clothes including more black jeans, an assortment of shirts, a navy blue hooded sweat shirt and a pair of black fingerless gloves. Misato had asked him about the particular selection of clothing, and he had chalked it up to personal taste, but the latter two he figured would compliment the physical training regiment he was preparing to put himself through. Shinji was determined to eliminate his shortcomings from the original timeline. And to do that he was prepared to push himself past his limits. As Shinji hit play on his SDAT and closed his eyes, he hoped that no nightmares would haunt him tonight.

***

"Is this my desire, to become one with Ikari-kun?"

Rei watched herself enable the self destruct device within her EVA.

"Rei, eject!"

"I cannot, or the A.T. Field will disappear."

A few moments later Rei and her EVA vaporized, taking the sixteenth angel with them.

Rei found herself waking in a cold sweat. She had never experienced what had been called a dream. She did not know how to react to the phenomenon. Sitting up, she felt something warm sliding down her cheek landing on her un injured her hand.

"Tears? Am I the one who is crying? Was that a vision of my death? It is possible, but it is more like it has already happened. A memory? But I am the second, of that much I am sure. Peculiar…"

Rei lie down once more, she decided that she would consult Akagi-hakase when she came in for an evaluation in the morning.

****************************The Next Morning*****************************

"Rei, that was what's called a dream."

Ritsuko laughed, she had never known Rei to have dreams. Gendou would undoubtedly want to hear about it, but the girl had seemed truly troubled about this dream. Ritsuko could relate, she had been plagued by nightmares as a young girl as well. However the albino girl's next question floored the scientist.

"Will pilot Ikari be coming to headquarters today?"

"Y-yes actually. He has a harmonics test and a few training sessions afterward."

Ritsuko would swear the blue haired girl brightened at the news even though her expression remained unchanged. Ritsuko shook her head.

'My mind must be playing tricks on me.'

***

Shinji hit the ground for what seemed the hundredth time. His first jujutsu lesson was becoming quite painful. The Instructor had to give it to the kid, he could take a beating.

"Well, Ikari-san, you've successfully outlasted Ayanami-san in how long you've been thrown around. Sure you don't want to give it a break for today?"

Shinji forced himself to his feet. He was feeling quite like a bag of tenderized meat, but he wouldn't let that stop him. He cracked a confident smile.

"No way."

"Then come."

**************************Commander Ikari's Office************************

Ikari Gendou was confused to say the least. Somehow his son had circumvented the first phase of the scenario. Now the boy was engaging in Martial Arts and Arms training, more specifically he requested to start with a sniper rifle. His actions told of some sort of foreknowledge. He had kept these small details from SEELE, as they didn't affect either Scenario, even Shinji's different attitude and abilities with Unit 01 didn't stall The Scenario.

But, somehow, it bothered him on a personal level.

***************************NERV Infirmary Wing**************************

"Wow, Ikari-san, did someone pulverize you with a wrecking bar?"

Shinji laughed, he recognized the nurse as the same one who had checked up on Rei.

"No, ma'am. My first Jujutsu lesson."

"Ah! Trying to impress a girl?"

Shinji blushed.

"N-not really."

The nurse giggled to herself.

"You check out, Ikari-san, you can put your shirt back on. By the way, Ayanami-san asked about you today."

This caught Shinji's attention, causing him to stop halfway from putting his shirt on.

"She did?"

The Nurse nodded.

"She wanted to see you again."

A smile crossed Shinji's face.

"She's really special to you, isn't she?"

"Yeah."

"Well you better get going. You shouldn't keep a lady waiting."

"Right! thank you…"

"Chise."

"Thank you, Chise."

The nurse smiled as Shinji ran out the door.

***

Within Moments, Shinji had arrived at Rei's door, after catching his breath for a moment, he entered the room.

"Good Morning, Rei-san."

"Good Morning."

Rei was standing by a window overlooking the Geofront, Shinji took a spot next to her.

"Shinji-kun, why do you visit me so often?"

Shinji flinched. Sooner or later the question was bound to come up. He would have preferred later, MUCH later.

"I…I care about you Rei-san. If I bother you, I can stop."

"No, I find your visits…pleasant"

They stared out the window a little while longer in silence.

"Shinji-kun…May I…may I hold your hand?"

The question caught Shinji off guard, but he smiled and pulled his hand from his pocket.

"Sure thing, Rei-san"

Slowly their hands reached out to each other's, tentatively feeling the other hand before fully clasping. Rei felt the warmth she felt when Shinji was around multiply tenfold.

Shinji just looked at her and smiled."

**************************One Week Later********************************

Shinji checked behind him, to make sire he was not being followed. He would not allow anyone, especially Section 2, to stop him in his urgent mission. He infiltrated the building in which his target was contained without detection. He held his precious package tight. Shinji steeled his nerves as he prepared to attack his target;

Room 402

He pushed the door open and was a immediately show what could be considered a disaster area. He shook his head and emptied the overfilled mail slot. With his keen eye fir junk mail he immediately tossed those into the trash bag that was part of his arsenal. The other mail was sorted and placed accordingly on Rei's table.

"Targets aquired."

Shinji next picked up all the stray clothing on the floor, bed and table and threw them into a second bag for laundry. Next up was the sweeping. Out came the broom, and Shinji went to work.

Within two hours, Shinji had completely scrubbed Apartment 402 from top to bottom, no dish was left unwashed, no plank of floor unmopped. All Shinji had to do now was the mountain of laundry occupying the bag to his left. After lugging the trash to the dumpster, Shinji pulled out his cell phone and dialed. The phone rang a few moments before the other end picked up.

"Katsuragi."

"This is Ikari, I need an extraction."

"Roger. ETA is ten minutes"

"Roger."

True to her word, Misato's Renault Alpine pulled up to the curb no more than ten minutes later. Shinji heaved the massive bag of laundry into the back of the blue car.

"So, Shin-chan, why are you doing this anyway?"

"If you'd seen her apartment before I started, you'd know."

"Are you sure its not because you 'Like' her?"

Shinji blushed.

"Its not like that."

Misato gave her charge a sly smile before putting the car in gear. She knew that Shinji had a heart of gold and he would do this sort of thing for a friend…Hell he'd do it for a complete stranger. The world didn't deserve him.

Within an hour, Misato and Shinji had returned to the apartment complex. Shinji hauling the now cleaned laundry back to Apartment 402, where he then proceeded to put it away.

Shinji checked his watch, Rei would be released from the Infirmary in a couple of hours, so he need to get to NERV.

****************************NERV Infirmary Wing*************************

Rei heard someone running down the hall and when Shinji skidded to a stop in front of her open door, she almost smiled.

"Shinji-kun?"

Shinji stood up straight after catching his breath.

"I'm here to walk you home, Rei-san"

"This arrangement is acceptable."

"You have all your things?"

"I have brought none."

"Then lets go, shall we?"

"Yes."

Shinji was only half surprised when Rei slipped her uninjured hand into his. Shinji chuckled thinking how his father was probably pulling his hair out about now.

Elsewhere in NERV, Gendou sneezed violently.

*****************************A Few Hours Later***************************

Shinji was grinning from ear to ear, Rei looked shocked

'As shocked as Rei can look, of course'

"Shinji-kun, you did this?"

"Well, Misato drove."

Rei turned to Shinji, somehow her apartment had gained some of his warmth. Even though he had only done something as simple as clean it, he had done so for her well being. Rei herself had never bothered cleaning as thoroughly as Shinji had, having been conditioned by Commmander Ikari to accept her meager apartment in its dilapidated condition. For the first time, Rei wondered if Commander Ikari thought of her as anything more than a tool to achieve his ends. Had she paid any attention to the nagging in the back of her head, she'd have had her answer. But at that moment, Rei did something she had never done before, she acted on impulse; wrapping her uninjured arm around Shinji. The hug surprised him, but he returned it nonetheless.

"Thank you, Shinji-kun."

"You're welcome, Rei-san."

***

"I'm home!"

Shinji walked into the apartment in more than just good spirits. His scenario was in play; the seeds had been sown, whether they bore fruit only time would tell.

"Welcome home!"

Misato noticed Shinji's good mood, and concluded that Rei must have actually reacted to Shinji's cleaning.

"So…?"

"What?"

"Did she like it?"

"That's my little secret."

"Oh really? Keep your secrets then, I'll just tell her all the dreams you have about her."

Shinji turned red as a tomato, he didn't have any dreams like that, he was sure of it.

"What are you talking about?!"

Misato burst into hysterical laughter.

'Oh, I'll get you for this one Misato, just wait until we meet Kaji."

***

Finally the day that Shamshel attacked had arrived. Shinji steeled his nerves whilst he dressed. He would cook breakfast, then leave a cold beer in a bowl of ice for Misato, knowing that she had just come from night shift. He grabbed the trash and hurried out the door so he could walk to school with Rei, as he had ever since he had started school. Their walks were always silent, but it was comfortable silence. Shinji still didn't know where they stood, but they were at least friends.

Shinji sat at his desk listening to his SDAT. On cue Suzuhara Touji entered the class and stopped by Aida Kensuke's desk, where he, Horaki Hikari and Touji were conversing. Shinji hit the stop button on his SDAT to hear what they were saying.

"-robot's pilot was stupid and reckless, because of him, my little sister got hurt."

Shinji flinched, he'd been afraid of that outcome. He knew what was coming and he would accept it.

*******************************Lunchtime********************************

"Hey, you."

Touji stalked up to Shinji, shaking off the feeling that the new kid had been waiting for him. Shinji turned around and Touji let his fist impact Shinji's face. Unlike in the original timeline when he had been beaten up, Shinji was able to maintain his footing.

"Sorry about this new kid, but I won't feel better unless I hit you."

"I'm sorry, It was my recklessness that caused your sister to get hurt. If it will ease your anger, feel free to beat me up as much as you want."

Touji stopped. At first what the kid had said sounded like self-pity, but it wasn't. Somehow Touji knew his words were sincere. He stomped back to Shinji and grabbed him by the collar of his shirt. Even as he wound his fist back, Touji couldn't bring himself to hit this kid a second time. Somehow he felt as if he knew this new kid. When the angel siren began to blare, Touji released Shinji's shirt.

"You better get going."

Rei ran up to Shinji as Touji and Kensuke were walking away.

"Shinji-kun, we most report to headquarters, immediately."

"Right…"

***

Shinji sat in the entry plug of Unit 01, as launch preparations were made. Shinji had asked Ritsuko to have his EVA equipped with a second progressive knife for this mission. She'd given him a quizzical look but had agreed to it nonetheless. Misato's voice came through the speakers of the entry plug;

"We're sending you up, Shinji-kun."

"Roger."

"EVA 01, Launch!"

Shinji prepared himself as the lift ascended. Upon reaching the surface, Shamshel switched to combat mode. As the final locks disengaged, Shinji locked his eyes on the fourth angel.

"Target Aquired."

Next Episode- Shinji battles Shamshel in a rematch. Ritsuko studies whats left and Shinji hangs out with his friends. But even as things look bright, there is a storm on the horizon.

Next Episode- **Ame** (Rain)

* * *

I apologize for not updating a hell of a lot sooner, but my laptop went kaput! I had to wait to recover my files and transfer them, which only happened recently. Hopefully it won't be as long until the next chapter, eh?


	4. Ep 3 Ame

Shin Seiki EVANGELION: Tamashi no Refuran/ Neon Genesis EVANGELION Soul Refrain

Episode 4: Ame (Rain)

Shinji stood, face to face with the enemy. A pallet rifle appeared from one of the weapons lifts to his side. Neither the angel nor the EVA budged, as if each was waiting for the other to make the first move. A full minute passed before Shinji quickly grabbed the rifle and dodged Shamshel's Energy Whips; doing an ukemi (quick dodge roll), and firing a few rounds at the Angel, knowing that it was ultimately useless. Misato's voice filled Shinji's ears, but he never took his eyes off of the enemy.

"Shinji you need to close the distance and neutralize it's A.T Field."

"Roger"

Shinji began running at Shamshel, strafing to avoid its energy whips, and letting out a few more bursts of gunfire, mainly to distract it as he closed the distance. Discarding the fire arm as he came into the proximity of Shamshel's A.T. Field. Opting instead for his prog knife. Unfortunately Shamshel was one step ahead of Shinji, wrapping its energy whips around Shinji's knife hand and flinging Unit 01 into a nearby building. Another strike from the Angel cleaved the building in two, nearly taking off the EVAs head in the process. Shamshel did not let up, as it resumed its assault even as Shinji was regaining his footing. Shinji had managed to recover his Prog Knife, returning it to its pylon, as he continued evading the Angel's assault.

In the Central Dogma, Misato watched as Shinji was pushed from had seemed a strong offensive to a rapidly failing defensive. When Shamshel managed to sever Shinji's umbilical cable, her mind began to race. Similarly, Ritsuko also found herself grasping at straws. There was a sharp intake of breathe from all in the Command Center when Shamshel managed to wrap its Energy Whips around Unit 01's ankle, flinging the EVA into the nearby hillside.

Back in the Plug Shinji recovered from the impact, glaring at the Angel as it closed the distance with impressive speed. Then Shinji remembered. Jerking his head to his left he saw Touji and Kensuke cowering between the third and fourth fingers of the EVAs left hand.

Ritsuko and Misato simultaneously noticed the boys.

"Who are those boys?"

Maya called up the records for Shinji's school, matching the two boys as Aida Kensuke and Suzuhara Touji.

"Shinji's classmates?!"

As the Scientist and Ops Director assessed their options, Shamshel struck out, Shinji grasping the energy whips in both hands.

Ritsuko made a split second judgement, for once acting on her conscience.

"Shinji hold the EVA on current commands and eject the plug, let them into the cockpit."

"Roger."

Misato glanced at her friend and they smiled at one another.

"I just hope the thought noise doesn't impair Shinji's ability to pilot."

"He'll be fine. I just know it."

The Entry plug partially ejected from the EVA and Misato's voice called out to the boys.

"You two, get into the plug! Hurry!"

Touji and Kensuke nodded and double timed it into the Entry plug. Shinji took a moment to switch off the comm unit as Kensuke bemoaned the loss of his precious camera. He had a plan, though it was a shot in the dark.

"Listen up you two, I need you to concentrate with me in order for this to work."

The two boys were unsure of what he meant but both Touji and Kensuke knew they had to do as the new kid said. Both boys nodded.

"Just tell us what to do."

Shinji switched his comm unit back on. With a mighty thrusting kick Shamshel was sent hurdling back into a building at the bottom of the hill. In the Central Dogma Ritsuko was staring at her monitoring equipment in disbelief. The introduction of the two boys hadn't produced any thought noise, on the contrary the Instruments were now registering a spike in synchronization.

"Shinji retreat for now."

"I can't do that, Misato-san, the Angel isn't just going to take a break while we try to regroup. I can take him!"

Misato stared at the counter for the EVA's internal battery, which was nearing shut down. Misato made a choice.

"Its game over if you fail, Shinji."

"I know."

"Sixty Seconds Remain until deactivation"

Shinji, Touji, and Kensuke tensed.

"NOW!!"

Unit 01 skidded down the hill toward its target.

"PROG KNIVES!!"

"Both Progressive Knives Deployed."

Shamshel lashed out with its energy whips, only to have them severed by the dual wielded prog knives.

"GRAB THE YOKES!!"

Touji and Kensuke did as instructed, grabbing the Butterfly Yokes alongside Shinji.

"Now Strike the core with everything you have!"

The Next few moments were a blur of slashes and stabs into Shamshel's Core. As the countdown neared the final ten seconds of activation, everyone in the Central Dogma held their breath. It seemed either sheer luck or miracle that the core shattered into dust just as the EVA ran out of power.

"Target and EVANGELION Unit 01 have gone silent."

Shinji let loose the yokes and sank back in his seat, releasing a relieved sigh. He turned to face the two boys with a smile.

"Thank you, both of you, I couldn't have done it without you."

-----------------------Central Dogma--------------------------

"There's no doubt about it, both of those boys partially synched with Unit 01. They have the potential."

Misato stared at Ritsuko in shock. She'd never heard of an EVA synching with more than one pilot at a time, much less three.

"Should we inform the Commander?"

"Not yet, I need to study the data from this engagement closer before I can draw any positive conclusions."

"I'll leave it up to you, Ritsu, keep me informed of your findings."

"I will, Misa."

* * *

It had taken an hour to retrieve Unit 01 from the field, and another half an hour to extract the entry plug. Currently the NERV Ops Director, The two boys, and the Third Children where in a small dimly lit room with dark walls. A Single Table with two chairs, currently occupied by the two boys, sat in its center. Shinji leaned against the wall, interested in what Misato had to say about all this. Misato herself stood opposite the boys and looked at them sternly.

"Well, you boys sure caused a mess out there."

"Sorry"

"You could have cost dozens of lives!"

"Sorry again"

"You endangered the pilot's life!"

"Sorry a third time."

The unified apology from Touji and Kensuke was rather amusing to the Third Children. As Misato continued her expression softened.

"However, you did help Shinji-kun defeat the Angel"

"Sorr- Wait what?"

"You two were a part of the first three part synchronization with an EVANGELION."

This caught Shinji's attention, the fact that Touji was able to assist him was predictable, after all Touji was the future Fourth Children, what intrigued him was that Kensuke had managed to partially synch with Unit 01 as well. This was entirely new, and he was unsure of how this would effect things.

"So what happens to them?"

"For now a pat on the back and a 'You're lucky the Commander wasn't here.'"

The two boys looked puzzled, turning to Shinji for clarification. The Third Children traced a line across his throat, the universal sign of "Your Ass Would Be Grass", though he had to restrain a smile as the two boys visibly paled.

"Shinji-kun, could you walk them home?"

Shinji nodded.

"Give me five minutes to change."

* * *

Touji and Kensuke trailed Shinji as they walked, heads hung low in shame. Shinji cast a look over his shoulder, noticing the downtrodden looks on the boys faces.

"Cheer up, it could have been worse. That was nothing compared to some of the lectures I've gotten."

"Huh?"

"You know her?"

"Well yeah,I live with Misato-san."

"You live with that babe?!"

"Yeah."

"You lucky son of a bitch!"

Shinji laughed. At least Kensuke and Touji hadn't changed. After the boys laughed for a minute, Touji's expression turned serious.

"Listen, Shinji, I'm... I'm sorry for beating you up earlier."

"It's alright. I don't have a little sister, so I don't know what its like to have one get hurt from someone else's stupidity, but I think that you were justified in what you did. I think, though, that I'd like it if we could be friends."

"Yeah, definitely!"

Touji halted, it was not sitting well with him that Shinji was willing to let him get off scott-free.

"Shinji, I won't feel right until you hit me back for beating you up earlier, justified or not."

"You sure?"

"Yes! Don't Hold Back!"

Shinji balled up his fist, and let Touji have it right in the gut, hard.

"Shit, you have (cough) one hell of a punch. (cough)"

Touji stood up and smiled, Kensuke already grinning from ear to ear. Shinji couldn't help but smile as well, the San-Baka-Trio had reconvened. And as they continued walking, Kensuke couldn't shake the feeling of familiarity.

"Shinji, I swear I know you from somewhere, are you sure we've never met, before you moved to Tokyo-3?"

Shinji sighed and slung his arms over his friends' shoulders with a smile.

"Maybe in a past life, Kensuke, maybe in a past life."

The San-Bake-Trio laughed collectively as they walked

-------------------------NERV Labs------------------------------

Ritsuko sighed and rubbed her eyes. She had been reviewing the data from the engagement with the Fourth Angel; the computer data and the actual footage of the battle, for hours now, with still no obvious answers presenting themselves. So far all she had managed to confirm was that the EVA did synch to all three boys, she had data readouts that confirmed that. What she didn't know is how or why the EVA suppressed the extent of synchronization of the two excess passengers. Ritsuko turned to her assistant and protege, Ibuki Maya, still hard at work analyzing the excess data.

"Maya I think we may have stumbled onto something here."

"Sempai?"

"I'm not sure, but until I have conclusive evidence, we _cannot_ tell the commander. You understand right?"

"Y-yes, sempai."

Ibuki Maya was no idiot, she knew that Commander Ikari would have the two boys eliminated if he found out. And the two boys seemed to be friends with Shinji. She didn't want to hurt the boy, not that she had a crush on him or anything.

Elsewhere in Tokyo-3, Shinji sneezed.

* * *

At the Katsuragi-Ikari residence the smells of cooking wafted through the air. Misato and Penpen sat on the couch, Yebisu in hand/flipper, watching the television. The ringing of the phone caught Misato's attention, as she leapt over the back of the couch to answer it.

"Hello, Katsuragi-Ikari residence."

"Misato?"

"Oh, Ritchan, what did you find?"

"I can't draw any conclusions until I have more data, Misa-chan."

"Hmm, that is a problem. Its not like we can just call Aida-kun and Suzuahara-kun in for a harmonics test. Damn it. We'll just have to hope that a small coincidence like this occurs again in the near future. Any good news?"

"Yes actually, the Magoroku Exterminate Sword prototype is already in development. Running with Shinji-kun's idea we also designed the Counter Sword. Some of his other ideas are being seriously considered. I tell you Misa-chan, that boy has his parents' genius."

Shinji would be glad to know that several of his plans were already in development.

"Well, I'm calling it a night, I'll see you on Monday."

"G'night Ritchan"

"Goodnight Misato, enjoy your day off."

As Misato hung up the phone, she remembered that she had promised to teach Shinji how to swim on her next day off. She smiled, she'd have to secure a pair of swim trunks for the boy, but in the end it would be worth it.

------------------------The Next Morning-----------------------

"Shin-chan, time to get up."

Shinji felt something made of cloth land on his face.

"What is this?"

"Swim trunks. I told you I'd start teaching you the next time I had a day off."

Shinji sat up and looked at Misato. His eyes almost bugged out when he saw the rather revealing two piece she was wearing, a pair of cut-offs covering her bottom half. He was also sure he had a minor nose bleed. After laughing at Shinji's reaction to her current attire, Misato backed out of the room.

"I'll give you some privacy, so you can get ready.

Shinji smiled.

"Right, I'll be out in a minute.

-------A Little While Later, NERV Recreational Facility-------

Shinji stood at the edge of the pool. His fear of water surfacing in full force. He swallowed hard and then looked at Misato, already waist deep in the shallow end of the pool.

"Come on in, we'll start simple. If you can take a beating from your Martial Arts Instructor and not complain, this should be a cake walk."

"If you say so."

Taking a deep breath, Shinji stepped into the pool. He moved slowly at first, forcing his fear of swimming back down into the shadowy depths from whence it came. Reaching Misato, his guardian smiled a reassuring smile and ruffled his hair.

"Okay first things first. I want you to lay back in the water and clear your mind, like you were meditating."

Shinji gave her a worried look.

"Don't worry I'll be right here the entire time."

Shinji swallowed the lump that had been forming in his throat and nodded. He cleared his mind in the fashion that his instructor had taught him, and laid down in the water. And he found that contrary to his firm belief, he didn't sink. He actually liked it, as it gave him peace, a contented smile took its place on his lips.

He floated like this for a half hour or so, until Misato was confident that he was comfortable floating, making the next phase easier.

"Okay lets move on to the next part, okay"

Shinji once again regained his footing and smiled, nodding.

-------------------In The Chambers of SEELE-------------------

Ikari Gendou sat calmly at a desk surrounded by several black monoliths, each inscribed with the word SEELE and a number.

"You were supposed to ensure that the core of the fourth angel survived in some manner Ikari, You have failed to do that. The Human Instrumentality Project hinges on our ability to create the S2 Organ possessed by the Angels."

"I was not present for the engagement with Target Codename:Shamshel, thus I could not give the instruction to preserve the core."

"No excuses, Ikari. Your performance as the head of the NERV has been very questionable indeed. Your selection of your own son as the pilot of Shogouki, his natural proficiency with the EVA. What have you told him, Ikari? What does the boy know?"

"I assure you, members of SEELE, that the Third Children knows nothing of the origins of the EVANGELION series, the core of Unit 01, or the Human Instrumentality Project."

"Lying in these Chambers is an offense punishable by death, Ikari."

"I am well aware of that, members of SEELE. That is why I say this with confidence."

"Beware, Ikari, we will not think twice about removing you from your position, if the demands of this organization are not met."

"That would be a folly. The Third will not pilot Unit 01 without my presence, and EVA 01 will not accept another pilot. You all know as well as I do the core of the EVA."

"You are a fool to think that you are irreplaceable, Ikari. And the Third Children, your son, is just as easily replaced. But for now, you needn't worry, we still have use for you. You are dismissed."

With these last words the holographic projection of Gendou disappeared.

"Ikari will Betray us, Chairman."

"I am aware of that 04"

"May advise we move forward with Contingency A."

"I second the notion. If Ikari does betray us we must be ready."

"Very well begin moving forward with Contingency A, if we work expediently they should be ready by the time Target Codename:Sandolphon surfaces.

--------------------NERV Commander's Office-------------------

Gendou sat at his desk a moment, fuming silently. When his subordinate, and former teacher walked in, Gendou made up his mind.

"Fuyutsuki-sensei, I have a request."

"Ikari?"

"Should anything unforeseen happen to me before the conclusion of the Scenario, have Shinji taken as far away from NERV as possible and hidden."

To say the request surprised Fuyutsuki was an understatement. The look of shock written on his former teachers was not wasted on the NERV Commander. The Sub-Commander nodded. Perhaps there was hope yet for his pupil.

-----------------Katsuragi-Ikari Residence--------------------

Shinji sat at his desk, recording everything that had happened so far, and calculating possible routes to take from these. So far, his scenario was coming along quite nicely. Outside the rain poured heavily. Misato had told him that Ritsuko was already working on the prototype of the Progressive Katana he had suggested, and was reviewing several other plans and weapons he had come up with. But the Magoroku was his crown jewel. It came to him while he had been watching an old, pre-impact movie, called _Yojimbo_, and he quickly designed the blueprints from what he knew of the mechanics of the Prog Knife.

And to top it off, Ritsuko had taken it a step further and designed an EVA sized Wakazashi, called the Counter Sword.

But that was only the surface, his destruction of Shamshel's core in the fashion it had been done was to keep it from falling into the hands of NERV and causing the events that would lead to the Thirteenth Angel. The other part of this involved convincing his father to transport Unit 03 by sea instead of air, because he was almost positive that the Thirteenth Angel had infested the EVA during mid-air transport, or else it would have gone on a rampage in the United States, before heading to Japan. Additionally, it would save EVANGELION Unit 04 from obliteration. Shinji was shaken from his thoughts by the ringing of his cell phone. The Display read _Touji_.

"Hey Touji, what's up?"

"Yo, I'm heading over Kensuke's for a while you wanna come? Its gonna be video games and junk food, man!"

Shinji chuckled. It had only been two weeks since the battle with the Fourth Angel, and already they were acting like they've been friends for years.

"Yeah sure, Just let me tell Misato that I'm going, and I'll be right over."

"Awesome, see you there, dude."

Shinji sighed as he hung up the phone, smiling. It was times like these that made his task worth it. That these people were worth saving.

* * *

Next Episode- Shinji pays his father a visit, and Rei gets her first encounter with the Enigma known universally as; Ice Cream. EVANGELION Zerogouki is reactivated, and the Fifth Angel appears. Hey wait, it couldn't do that before.

Next Episode- Kaminari (Thunder)

* * *

Author's Notes- I apologize to the fans of this story for taking so long, I had to write this chapter six times before I was happy with it.

And on another note I'm just gonna get this out there now. Any OoCness that is present is intentional. While I am currently skirting the canon line, don't expect it to stay that way for long. I will be pulling in ideas from all over the EVA-verse, not just the Anime. I can guarantee there will be times that I will lose fans of this story just for some of the ideas I'll be using. Any and all relationships aside from Shinji/Rei is free game right now, though mind you I won't be doing anything insane like Misato/Fuyutsuki are anything to that effect. But still, they'll be some crack in here. But please bear with it, I will do my best to make it worth it in the end

Thanks

* * *

**EDIT 1**- I changed the preview of the next chapter a little bit.

**EDIT 2**- Fixed some spelling errors, and fixed some of the punctuation.


	5. Ep 4 Kaminari

Shin Seiki EVANGELION: Tamashi no Refuran/ Neon Genesis EVANGELION: Soul Refrain

Episode 4- Kaminari (Thunder)

The sound of gunfire echoed through the firing range, as its sole occupant reloaded the sniper rifle he was practicing with. Shinji lifted the rifle again, staring down the scope at his target, at least 400 or so feet at the end of the large shooting range.

'Just a few more weeks until that floating bastard shows up.'

Shinji squeezed off another round. He then pressed a switch that backed the target up an additional hundred feet.

'Try not to get fried this time, Ikari.'

Shinji pulled the trigger again, the round finding its target.

--------------------NERV Infirmary Wing-------------------------

Rei sat in a hospital room, quite unremarkable as it was composed of four walls of equal length and height with a dreary off-white color, and contained only a bed, a small table and a vase full of flowers sitting on it. The only source of light coming from a fluorescent light fixtures overhead and the room had a faint odor of chemicals used to cleanse the room of unsanitary substances and particles. She so far had been waiting for twenty three minutes thirty seven seconds and counting for the physician that was scheduled to remove the cast on her arm. Exactly thirty minutes forty six seconds after her arrival at her appointed time a man of obviously advanced age hobbled in carrying a Stryker Cast Saw. Looking over his glasses the elderly physician smiled the pale skinned girl.

"How are you this morning, Ayanami-san?"

"My current state of health is within acceptable parameters."

Silence reigned for a moment, the old man trying to figure out the aloof young lady sitting in front of him.

"Doctor, please proceed."

"Yes, of course."

The doctor started up the cast saw and made two cuts along the sides of the cast. A little less than three minutes later, the cast was off.

"All done, you're free to go, Ayanami-san."

Rei gave a slight nod, standing up and leaving the rather suffocating space of the hospital room. Navigating through the various halls and corridors that The NERV HQ consisted of, Rei did not expect to encounter the Third Children. She took note of his attire, different from his usual garb of his Tokyo-3 Municipal Junior High School standard uniform. Instead, he was dressed in black jeans, a blue hooded sweatshirt with black fingerless gloves. He also wore a surprised look on his face.

"Rei-san, what are you doing here?"

"I reported to the Infirmary Wing to have the cast on my arm removed, Shinji-kun."

Shinji's eyes went down to Rei's arm, noticing the cast was missing.

"That's great, Rei-san!"

A smile lit Shinji's face, sending that feeling of warmth through the First Children.

"Do you mind if I walk with you?"

"That would be acceptable."

And so the First and Third Children began walking together, the usual comfortable silence reigning between them. As they reached the exit of NERV HQ an idea struck Shinji like a bolt of lightning.

"Hey, Rei-san, let's go get some Ice Cream."

"Ice...Cream?"

Rei was puzzled. She knew that Ice was water brought to a state of solidity, and that cream was extracted from female members of the bovine species through a process called "milking" but she was at a loss as to the two had in common.

"What is...Ice...Cream?"

Shinji halted and turned, looking into Rei's eyes to see she genuinely did not understand the concept of "Ice Cream."

"Oh. HELL. No."

Shinji knew that he must fix this, and fix this immediately. He grabbed Rei by the wrist and set himself on a mission to find the nearest Ice Cream vendor. Little did Shinji know as he pulled the confused First Children along behind him that someone was watching the live surveillance feed for that section of NERV.

-------------------Twenty Minutes Later-------------------------

It had taken some hunting and a stop at an ATM machine, but Shinji had finally located his target, which he now approached, a confused Ayanami Rei in tow.

"Good Afternoon, young man, what can I get for ya today?"

"Hmm, lets see, you've never tried this so we should start simple. One vanilla cone,"

Shinji glanced over his shoulder.

'One on the bench behind the newspaper, one by the fountain, one walking the dog, and one nonchalantly sitting on the hood of his Sedan.'

"Make that five. And For me a chocolate cone, please."

"Hahaha, quite a tall order there!"

The vendor went about preparing the order, and moments later handed Shinji six cones, which Shinji positioned between his fingers, three in each hand.

"I'll be right back, Rei-san."

The Section 2 Agent sitting on the bench twenty feet from the two pilots, feigning reading the newspaper, was quite shocked when the Third Children approached him.

"Here, I bought this for you. I didn't know what flavor you liked so I went with the mainstay of Vanilla."

The Agent hesitantly took the gift that the Pilot had given him, curious as to how his cover had been blown. Shinji repeated this process with the three other agents that had been tailing them since leaving NERV, each exhibiting a similar reaction. After a few moments Shinji re-joined Rei at the Ice Cream stand, fetching some of his cash out and handing it to the vendor.

"Keep the change."

The vendor grinned at the boy, then looked at the amount.

"S-son, this is-"

"I know how much is there, keep it."

Shinji punctuated his answer with a smile, before returning his attention to the First Children; who was now even more confused than before. He handed her the remaining Vanilla cone, which she accepted with curiosity. Rei watched as Shinji began to consume his own frozen confection and decided that she should follow suit. The assualt of pleasant flavor on her until then deprived taste buds was amazing. She eagerly took another bite, more flavor coursing its way past her taste buds.

"You like it?"

"Yes, it is...enjoyable."

"I'm glad."

"Though something strikes me as curious, Shinji-kun."

"Oh? What's that?"

"You were able to identify the Section 2 Escorts that have been assigned to follow us discreetly, how?"

"Did they look that discreet to you, Rei-san? The suits and sunglasses, obvious giveaways. Lets also take into account that none of them moved in any way, save for breathing, the entire time I was at the stall. They stick out like sore thumbs."

Rei thought about this for a moment, and found that Shinji's logic was without error.

"You are well versed in tactical assessment of a situation, Shinji-kun."

This caused Shinji to chuckle a little and smile even wider at the albino girl.

"I'll take that as a compliment, but I don't think I'll start campaigning for Misato's job anytime soon."

"Why would you attempt to seize Captain Katsuragi's position"

Shinji sighed.

"It was a joke, Rei."

"I see."

"Come on, I'll walk you home."

Rei nodded and the two pilots resumed their walk, as Shinji shouted over his shoulder at the Section 2 Agents.

"Hey, you guys coming or what?!"

-------------That Afternoon, Ikari-Katsuragi Residence----------

Shinji sat in his room, playing his Cello and deep in thought. As the notes of Bach's Cello Suite no. 1 filled the air he thought about what to do next concerning the First Children. He did not want to rush things. The thought processes and his cello playing came to a halt as his cell phone rang. He reached into his pocket an pulled out his phone.

"Ikari."

"_Shinji."_

Shinji's eyes widened.

"Father?"

"_I wish to see_ _you, I have sent a Section 2 Car._"

"I understand."

"_Good_. {click}"

As Shinji stared at his phone, his mind was awash in worry. Why had his father called him, on his cell phone, _personally_. This did not sit well in the younger Ikari's mind. Then a devious smile that would not look out of place on the face of his father formed on Shinji's face.

A few moments later Section 2 came knocking on the apartment door, which Misato promptly answered. Seeing the agents, Misato switched from _Fun-loving Care-free Misato_ to _Ops. Director Misato_ mode.

"What is this about, Gentlemen."

"We are here to-"

"They're here for me, Misato-san."

"You?"

Shinji nodded.

"Him?"

The agents nodded.

"Don't worry, Misato-san, my father just wants to have a little chat."

The smile on Shinji's face did nothing to alleviate her worries.

"Be careful, Shinji-kun."

"I will."

Then Shinji realized that the two Agents were half of the group of four from earlier.

"Oh, hey guys, did you enjoy your ice cream?"

The agents now got visibly nervous, sweat forming on their foreheads. Misato stared at the agents as they and Shinji walked off.

"Ice cream?"

----------------------An Hour Later, NERV HQ--------------------

Gendou sat at his desk, hands bridged in front of his face. He knew that the Third Children would be arriving any moment now. He mentally composed himself. And true to his prediction, Ikari Shinji walked into his office mere moments later, a smile on his face and his hands implanted in his pockets.

"Good Afternoon, father. How are you today?"

The friendliness of the greeting caught Gendou off guard.

"You wanted to speak to me?"

This prompted Gendou to clear his throat, and recompose himself.

"Yes. I saw you exiting the Geo-Front with the First Children in tow. What are your intentions with Pilot Ayanami?"

"Rei-san? I don't have any intentions, none that I'm aware of anyway."

"The First has told me about this 'friendship' of yours."

"So I gathered."

"Where did you and the First go?"

"To get ice cream."

"Ice Cream?

"She'd never had it, so I bought her some. I'll have you know she enjoyed it."

Gendou paused for a moment, observing his son. The boy's smile had not faded an inch since his arrival.

"Why are you smiling?"

"I'm happy to see you, I am your _son_ after all."

The look of shock was now visible on Gendou's face.

'Scored a direct hit. Ikari you are genius'

"You know father, I think we were reunited on the wrong foot, I'd like to fix that."

"I do not have time to-"

"Its not like I'm asking for you to take me on a fishing trip or anything. I'd just like to talk with you more often. You know, get to know you better."

'And Ikari completes a second bombing run with pinpoint accuracy.'

"We shall see. Now back to the matter at hand. Why do you seek the attentions of the First Children?"

"I'm her friend."

"We've established that, the question is why?"

"Because she looks like she needs someone to talk to. I'm just filling the role."

'Complete bullshit, but he doesn't need to know that.'

"Do you disapprove?"

Gendou thought for a moment. Rei knew not to divulge any information regarding The Scenario or her origins to anyone under any circumstances. In the end it mattered little as long as it did not effect The Scenario.

"No."

Gendou paused for a moment.

"How did manage an 85% synchronization in your first sortie with Unit 01."

"Chalk it up to extreme concentration. I was determined to beat that angel as quickly as possible. You've undoubtedly noticed my average score in harmonics tests are on average in the mid-sixties."

"And knowledge of the A.T. and possession of the Progressive Knife?"

"Asked one of the techs on the way to the plug. He told me about the defensive capabilities and informed me of the location of the progressive knife. Good thing too, or I probably would have just fell on my face."

"I see. You may go now."

Having made the first move in the chess game of psychological warfare with his father, Shinji turned to leave and as he did so he smirked.

------------------Apartment 402, A Few Hours Later--------------

Rei lay on her bed, thinking about the events of earlier in the day, when Shinji had taken her for ice cream. She had found the frozen treat quite good, informing Shinji that she would accompany him again should he so choose. He had laughed and confirmed that he would indeed like to.

"Shinji-kun..."

A small smile found its way across her lips. The Commander's son had not been in Tokyo-3 long, but already he had dispatched two angels. He always escorted her home, even though he lived in the opposite direction. He had gone out of his way to improve her living conditions, for no reasons better than her comfort and well being.

Rei looked at her hand, twice she had held Shinji's hand in her own. She; whom had never had any particular desire to interact with anyone, other than the commander, liked the feeling of warmth that emitted from Ikari Shinji.

-----------Tokyo-3 Municpal Junior High, the Next Day-----------

Shinji sat on the roof of the School; Touji to his left, Kensuke to his right, a bento on his lap. It was lunch time and Shinji noticed his two friends, who normally wolfed down their meals had hardly touched their bentos.

"Is something the matter?"

"Shinji, me and Kensuke, we gotta ask you something."

"Yeah, go ahead."

"Are You and Ayanami going out?"

The mouthful of rice that was in Shinji's mouth just shot out at incredible velocity.

"What?!"

"You see Kensuke has a friend of a friend who says.."

"In other words Kensuke followed me."

Shinji looked at Kensuke, who refused to make eye contact, proving his theory.

"To answer your question, no we are not going out. I took her for some ice cream as friendly gesture, as she had just had her cast removed."

"Told you so."

"Shut up, Touji."

"Besides, no one can melt the Ice Queen, right Shinji?"

"Well, I don't know about that."

"Huh?"

"What do you mean, Shinji?"

The bell signaling an end to lunch sounded, cutting off any chance for Touji and Kensuke to hear clarification from the Third Children.

--------------------------After School--------------------------

Shinji had his briefcase slung over his shoulder as he walked, SDAT headphones in his ears. He had a million and one thoughts going through his head, as had become his new normal. And while he was confident that his plan was going well, Shinji knew that everything sat on the proverbial razor's edge. Everything had to be calculated and in truth, Shinji found himself using parts of his brain he'd never known existed before the beginning of his Scenario. Shinji sighed and rubbed his temples with his free hand. His SDAT was between tracks when he heard a familiar voice.

"Shinji-kun?"

Seeing Rei standing beside the gate, Shinji pulled the headphones from his ears. Usually Shinji had to look for Rei, not the other way around.

"Were you waiting for me Rei-san?"

Rei gave a single nod.

"Oh. Sorry if I kept you waiting."

"I…was not waiting long."

"Heading home?"

"No, I must go to Headquarters this afternoon."

"Ah."

"Will you…walk with me?"

"Of course."

As the two pilots left, the two spectators leaning against the school building retrieved their briefcases and readied to leave.

"Man, they've got it bad."

"You think they know, Touji?"

"Knowing Ayanami, probably not."

"What about Shiniji?"

"He's not stupid."

"Should we try and help, Touji?"

"For right now, I think its best to let things be."

Kensuke burst out laughing.

"What?!"

"You know, its times like this that your heritage shows."

"What's that supposed to mean?!"

"Think about it Touji, both of your parents and your paternal grandfather, all scientists. You're smarter than you let people think."

"Sh-shut up! Don't let people hear you say that!"

-------------NERV Headquarters, Akagi's Office------------------

"Well, Rei, you appear to be in peak physical condition. And your harmonics test results were the same as normal. All in all you'll be ready for the reactivation test scheduled in a few weeks"

Ritsuko swiveled the chair to look at the First Children. She noticed the look of confusion on the normally expressionless girls face. She had no love for the girl standing in front of her, but she did not want anything to stand in the way of the pilots ability to pilot.

"Something wrong Rei?"

"Akagi-hakase, what does it mean when being around a person makes you feel warm within, and all that is required to trigger this feeling is a smile?"

Ritsuko's chair fell backwards, she was completely unprepared for the question, much less the source asking it. Staring at the ceiling for a moment Akagi Ritsuko ran the last minute and thirty seconds through her head, just to make sure she was not hallucinating. She stood up and fixed her chair, looking at the First Children with a sense of curiosity. She took a deep breath, ordering her thoughts before responding.

"Rei, why do you ask?"

Then Ritsuko almost fell to the floor again, as a phenomenon that she had never bore witness to manifested itself on Rei's face. Ayanami Rei was blushing.

'Oh, _this_ just got interesting.'

---------------NERV Headquarters Commander's Office-------------

Ikari Gendou stood in his office, staring out the large window over looking the Geo-Front. His son's words still stuck in his head. It truly puzzled the elder Ikari. After all that had happened, his son still wanted to know his father.

"Ikari? Is something troubling you?"

"No, sensei, I was just thinking about Unit 00's next activation attempt."

"I see. Do you think we will be successful this time, Ikari?"

"I believe so."

-----A Couple of Weeks Later, Tokyo-3 Municipal Junior High-----

"You think you can take me?"

"Don't get cocky, Mr. Badass-Pilot."

Shinji danced around Touji, avoiding the members of the other team as he headed toward the hoop on the other end of the court, and with a bit of effort managed to sink a basket quite like a certain pre-impact American Basketball star. Touji was both shocked and impressed.

"Alright, Ikari's team wins this round. Next two teams hit the court!"

As the Gym Teacher ordered, Shinji and Touji left the court and sat by the wall.

"Good game, Shinji."

"Yeah, you too."

After a while Shinji's gaze drifted up to the pool area, where the girls of the class currently were. Sitting away from the others against the fence was Rei.

"Whatcha looking at there, boss?"

"Ayanami, I bet."

"Yeah, Ayanami's _breasts_, Ayanami's _thighs_, Ayanami's-"

"Will you two cut it out?"

After scolding his friends, Shinji returned his gaze to the First Children. Rei turned her head to meet his gaze, offering a small smile and a wave rendering Kensuke and Touji speechless.

"She smiled at him?"

"And waved?"

"Yeah, So? What's so odd about that?"

"Uh, hello, Ayanami is the Ice Queen!"

"Do you guys have a nickname for every girl you know?"

"Uhh...."

Shinji sighed.

"I thought so."

-----------------At The Same Time, NERV HQ----------------------

"So, learn anything new, Ritchan?"

"Well, while having the Cores to study would have been ideal, we have been able to learn a few things about the enemy, Misato."

Ritsuko punched in a few commands on her field terminal, bringing up the composition analysis for the third and fourth Angels. On the screen flashed the number 601.

"What does that mean?"

"It means 'Cannot Be Analyzed"

"So in other words you have no idea?"

"Don't be insulting."

Ritsuko entered another command.

"Notice anything?"

Misato's eyes widened.

"While the Angels' composition is made up of a type of matter that is made up of particulate and wave properties; like light, the Angels' inherent wave pattern is a 99.89% match with Human DNA in terms of arrangement."

"Oh my..."

"We'll be busy for awhile that's for sure, with all this data to sort through."

"Well, that sucks."

The two friends took a sip of their coffee.

"Well before you get buried up to your eyeballs, why don't you join Shinji and I for dinner tonight?"

"Alright, I'm eager to see if your claims of his culinary skills are true."

---------------That Night, Katsuragi-Ikari Residence------------

Ritsuko sniffed the air. The scent was heavenly, and her taste buds were getting excited.

"Shin-chan! Is dinner ready yet?"

"Almost Misato-san."

A few minutes later dinner was served and Ritsuko was forced to admit, Misato was right for once.

"You know, Shinji, I'm tempted to steal you for myself."

"Back off sister, Shin-chan is mine!"

Misato emphasized her statement by hugging Shinji tightly to her chest. This earned a laugh from Ritsuko.

"Oh, I almost forgot."

Ritsuko went digging in her purse and pulled out a rectangular piece of plastic.

"Shinji could you do me a favor?"

"What is it?"

"I meant to give this to Rei, when I last saw her, but with all that's been going on it just slipped my mind. Its her Renewal card. Could you deliver it to her before reporting to headquarters tomorrow?"

"Sure."

Shinji took the card and looked at it. Ritsuko and Misato noticed the look of affection on Shinji's face as he stared at the card.

"Staring at Rei's picture are we?"

Shinji snapped back to reality.

"What are you talking about?"

"You've been staring at her picture for the last five minutes."

"Ritchan's right, you were."

"Well...I...uh."

Misato giggled at the cuteness of the situation.

"You've got an official excuse to go to Rei's place now, this is your big chance."

Shinji sighed, he would have to put up with Misato's teasing for the rest of the evening, but in the end, he knew it was worth it.

------------The Next Day, Rei's Apartment Complex---------------

Shinji stood before Rei's apartment door. He knew that if he walked in now, she'd just be getting out of the shower, and that was a fiasco he'd rather not repeat. After waiting five or so minutes until he was sure that enough time had passed, Shinji gave Rei's door a few hard knocks.

"Rei-san. Its Shinji-kun."

The door opened, and there was Rei, wearing naught but a towel. Shinji's brain stalled out as the blood rushed to his face.

"Shinji-kun, what brings you here?"

"I...uh...that is...uh...what was it? Oh...th-the card! Right the card...your renewal card...damn it where was it..."

As Shinji fumbled through his pockets looking for the Renewal Card Rei proceeded to dress. By the time she was finished, Shinji had found the card, and his brain had restarted.

"Here, your card has been renewed. Ritsuko-san asked me to deliver it to you."

Shinji handed her the card with a smile. Side by side the two pilots began walking to NERV headquarters, arriving a half hour or so later.

"Rei-san, Unit 00's Activation Test is today, right?"

"Yes."

"Are you scared?"

"Why?"

"You might get hurt again."

"Don't you have faith in your father's work?"

"Rei-san, I have faith in you, and that's all that matters for me. If you believe that everything will work out, then so do I."

The pure honesty behind the statement caught Rei a little off guard.

"Th-thank you...Shinji-kun."

Shinji gave her a parting smile as they headed thier seperate directions.

------------------------An Hour Later---------------------------

Rei sat in the entry plug of Unit 00, thinking about the words that Shinji had said. And her response to them.

'Words of gratitude, I have never used them before, not even with the Commander, and yet I find myself using them quite frequently with Shinji-kun.'

As if to answer her thoughts, said Commander's voice came through the speakers of the Entry Plug.

"Rei are you ready?"

"Yes, Commander."

"We will now commence the Unit 00 re-activation experiment."

In the control room, Ritsuko turned to her assistant and protege, Lt. Ibuki.

"Initiate first stage connection."

Shinji listened as the control room bustled with the technical lingo involved with the experiment.

"Connecting main power supply"

"Activation Voltage has passed the Critical point"

"Shift format to Phase 2."

"Connecting pilot to Unit 00."

"Opening Circuts."

"Pulse and Harmonics are normal"

"No problems detected in synchronization."

"All nerve links completed."

"Central Nervous System elements are nominal."

"Re-calculating, no error corrections."

"Checklist is satisfactory up to 2590. Approaching absolute borderline. Borderline cleared, Zerogouki has been activated."

Shinji finally exhaled the breath he'd been holding throughout the proceedings.

"Beginning Interlock Test."

Just then the phone that directly connected to the Central Dogma rang, Sub-Commander Fuyutsuki answered.

"Fuyutsuki. I see. I will inform the Commander"

Hanging up the phone Fuyutsuki turned to Gendou.

"Ikari, an unidentified flying object is approaching. It is likely the Fifth Angel."

"Stop the Test. All personnel, Alert Status Level One."

Shinji knew that the Fifth was here, it was time to dance. He turned to Ritsuko.

"How soon can you have Unit 01 ready?"

"U-uh..."

Ritsuko turned to Commander Ikari.

"Answer the question, Akagi-hakase."

"I-It'll be ready in 380 seconds."

"I'm heading there now."

Gendou nodded to the Third Children.

-------------------Six Minutes Later----------------------------

"Unit 01 is beginning the launch sequence. Releasing primary lock bolts"

Shinji steeled his nerves.

"Release confirmed"

"Roger, Releasing secondary restraints."

Shinji looked over to one of the catwalks and saw Rei standing there watching the pre-launch sequence. He smiled, though he knew she couldn't see it.

"EVA 01 is ready for launch"

Up above Ramiel, the Fifth Angel settled into position directly above the Geo-Front. In the Central Dogma, Misato issued the Launch Order. Ramiel felt something coming and along its equator energy began to build. On the bridge Lt. Aoba Shigeru picked up the reading.

"We're detecting a high energy reading from inside the Target!"

Misato jerked her head towards the Lt.

"What?"

On the screen Shinji shouted to the Ops Director.

"Blow the Pylon Clamps!"

"But Shinji-kun, at that velocity, you'll be launched into the air at high speeds!"

"Its better than getting nailed with whatever that thing is about to fire at point blank range!"

Misato turned to Maya.

"Do it!"

"Roger!"

On the lift the Emergency releases on the lifts Pylon Clamps gave way.

"Emergency Overide Confirmed, Unit 01 restraint status is free."

Aoba continued to report on the Enemy's status.

"The circumference area is accelerating! Its converging!"

As the Lift reached the surface Unit 01 was launched into the air, completely dodging the first beam. What happened next, though caught Shinji off guard. Ramiel shifted its shape, its core free floating with what appeared to be a focusing mirror and three pyramid like points just in front of it, and aimed directly at Unit 01.

"Well that's new."

* * *

**Next Episode**- Shinji does his best to fight off Ramiel's first wave, but when Unit 00 is launched in a desperate attempt to give Shinji back up, Shinji puts himself in the way of a the blast meant for the First Children. Misato conceives The Futago-Yama operation, all the while worrying about Shinji's condition.

Next Episode- **Kokoro** (Heart)


	6. Ep 5 Kokoro

Shin Seiki EVANGELION: Tamashi no Refuran/ Neon Genesis EVANGELION: Soul Refrain

Episode 5- **Kokoro**(Heart)

Shinji found himself looking down the proverbial gun barrel of the Fifth Angel, shocked over this new development. However he was shaken from this stupor by the voice of Lt. Aoba.

"The Angel is preparing for a second shot!"

"Shinji-kun, you've got to dodge!"

Shinji willed the EVA to curl into fetal position, then throw its weight backwards. In what seemed almost an impossible feat, considering the EVAs size, Unit 01 somersaulted in the air and landed back on its feet, missing Ramiel's second shot. Reconfiguring its shape again, with the three pyramids now fused into one lengthy pyramid Ramiel recalculated its weapon's trajectory. Not giving the Angel anytime to charge its weapon, Shinji began to move quickly up one of the battlements. He knew he had no chance against this Angel at close range. Misato watched helpless as Shinji dodged and evaded the Fifth Angel's onslaught, the enemy now having resorted to small concentrated Particle Bursts fired at a rapid clip, much like a machine gun. Then the Commander's voice came from above.

"Prepare EVANGELION Unit 00 for launch."

-------------------Moments Later, The EVA Cages-----------------------

EVA-00 was being moved into position, after having been extracted from the Lab. She knew that for Commander Ikari to give the order to Launch Unit 00 so soon after its re-activation test, the situation on the surface must have been dire. The Commander's voice crackled over the Entry Plugs speakers.

"Rei, The Third is currently pinned down by the Angel's attack. Upon reaching the surface you are to use this distraction to attack while the enemy's core is exposed."

"Understood"

----------------------------Central Dogma-------------------------------

"Ikari, you know she's not ready."

"We have no other options. If this will lead to the defeat of the Angel, then I will do what must be done, Fuyutsuki-sensei."

Below, Misato watched the screen displaying the battle, Shinji barely dodging another shot.

"Unit 00, Launch!"

-----------------------------The Surface-------------------------------

Shinji heard the order and jerked his head toward the screen displaying Misato's face.

"What?! Misato-san, Unit 00 just reactivated, there's no way she's ready!"

"Shinji-kun, you can't fight this one alone! We're sending Rei as back-up!"

Shinji only had a moments notice as the Yellow armored EVA reached the surface. However, the Fifth Angel had sensed this and now came about to fire on this new target.

"SHIT!"

Shinji willed Unit 01 to run as fast as possible, ejecting his umbilical cable at the same time. Back in the Central Dogma, there was a spike in his synchronization similar to his fight with the Third Angel. With only a split second to react, Shinji position Unit 01 between Ramiel and Unit 00 and expanded the A.T. Field to maximum. The Particle Beam slammed into the A.T. Field, physically shoving Shinji's EVA into Rei's.

Within Unit 00, Rei was stunned. Shinji had put himself in harm's way for her sake, and once again she found herself without answers to the numerous questions materializing in her head.

"The Angel's Particle Beam is too strong! Unit 01's A.T. Field is failing!"

Misato whipped around to stare at Lt. Ibuki.

"What?!"

On the surface, Shinji knew he could stave the beam off no longer.

"AH... FUCK!!!"

As the curse left Shinji's lips the beam tore through the A.T. Field, slamming right into Shogouki's chest armor. Shinji's screams of pain echoed through out the Entry Plug of Unit 00 and the Central Dogma.

"Blow the Lift Bolts! Bring them back down!!"

The technicians on the bridge did as they were ordered, and with a small controlled explosion, the lift dropped at a high rate of speed, Rei forcing her EVA to break the arm restraints to catch the collapsing Unit 01. The shock of the lift's crash landing nearly toppled both EVAs, but the First Children was able to keep her footing. In the Central Dogma, Misato was was panicking, demanding information on the pilot from Lt. Hyuga Makoto.

"How's Shinji-kun?"

"He's Alive. Unit 00 and Unit 01 are en route to the Seventh Cage."

Misato turned to Ritsuko, panic still in her voice.

"I'm going to the cage, please take over for me."

After receiving word that both EVA's were secured, Ritsuko turned to Lt. Hyuga.

"What's the status on the pilots?"

"Rei is unharmed but Shinji's brainwaves are erratic! His pulse is very weak!"

"Increase life support to maximum power. Give him a Heart Massage."

On Hyuga's screen, Shinji's body jumped as the electric shock was administered.

"Pulse Confirmed!"

"Force Eject the Entry Plugs! Hurry"

----------------------------EVA Cage Seven------------------------------

Misato arrived in the cages just as the LCL was discharged from Unit 01's Entry Plug. As Rei exited Unit 00's Entry Plug, she could only watch helplessly as machinery was used to extract the command module from the Entry Plug of Unit 01, blood pouring from Shinji's nose. She and Misato arrived at Shinji's side just as he was being loaded onto a gurney, Both followed the incapacitated boy as far as the Emergency Room Doors. It was then that Misato noticed Rei's presence.

"Rei, what are you doing here?"

"I am...concerned for Shinji-kun's health."

This brought a small sympathetic smile to the Ops. Director's face.

"Rei?"

"Yes, Captain Katsuragi?"

"Could you do me a favor and stay with him until they move him?"

"Yes."

----------------------On the Surface--------------------------------

Sensing no more threats in its vicinity, the Fifth Angel returned to its original eight sided shape, extending a drill from its bottom most point, beginning a slow process to reach the Geo-Front.

----------------------Central Dogma----------------------------------

Misato returned to the Bridge, noticing the Commander's absence. Ritsuko, Lt. Ibuki, Lt Hyuga, and Lt. Aoba all looked to her as she walked in. Maya was the first to speak up.

"H-how is he?"

"Shinji-kun will be fine, I have Rei down there with him, with orders to inform me as soon as he's in the clear."

She noticed that the Three Bridge Techs and the Doctor all had looks of relief on their faces.

"Alright, its no time to get sloppy, lets start going over our options."

"Roger!"

The Three Bridge Tech's swiveled in their chairs back to their consoles.

"You know, Misato, its amazing how that boy has rubbed off on everyone around here."

"Even you, Ritsuko?"

The scientist only offered her friend a smile.

"Maya and I have to get to work patching up Shogouki."

"Make it happen, Akagi-hakase."

Ritsuko nodded to Misato, motioning for Maya to follow. As another Tech filled Maya's spot, Misato began to formulate plans.

-------------------------Commander's Office-----------------------------

Ikari Gendou was in a very unprofessional position, perched over a toilet as he once again emptied the contents of his stomach, the Sub-Commander by his side, rubbing his back.

"I do not understand what has come over me."

"Ikari, you just watched your son nearly get cooked alive."

"Sensei, I have never reacted like this. The Scenario... it should be all that matters to me..."

"Ikari, no matter what has happened these last eleven years, you are still the boy's father. And in your own way, you do care about your son."

Gendou offered nothing in response to the comments by his old college professor, once again vomiting into the toilet bowl.

------------------------Inside Shinji's Head---------------------------

Shinji found himself sitting in a train, quite like the ones that coursed through Tokyo-3 and the modern Japanese countryside. The train was completely devoid of passengers, except for himself.

'This again, huh? I guess I could say this is my "Train of Thought."'

Shinji laughed dryly, Resting his head against the back of the seat and staring at the ceiling.

"Yeah that was lame."

{You got hurt again}

Shinji looked forward and saw an exact duplicate of himself, sitting with his head bowed, hands clasped between his knees.

"Comes with the job. That's why we get hazard pay."

The Other-Shinji looked up at him.

{I thought you didn't like pain.}

"I don't."

{And yet, you let yourself get hurt.}

"When Kaworu gave me the choice to fix things, I knew that I would be hurt. But for once, I knew I had to think beyond myself, and what I wanted."

{So you're only doing this because Kaworu asked you to?}

"Not at all. I'm doing this because its the right thing to do."

{Aren't you scared?}

"Of course I am, I'm terrified. But that doesn't mean that I'm going to run away"

{But if you run away, everything will be alright, you won't get hurt. Everything will just stop hurting you, and you'll be happy.}

The Other-Shinji smiled a pathetic smile at Shinji, and something in him just snapped. Shinji bolted upright and stomped across the aisle and yanked Other-Shinji out of the seat by his collar, a look of rage set on his face. Shinji realized his current resemblance to Touji, the second time Touji had hit him in the original time-line.

"You are pathetic, you know that? And you know what sickens me the most? That you are a part of me! I've spent my whole life running away, and I'm sick of it! I will **NOT** abandon those precious to me again."

Without a second thought Shinji punched his other self across the face, sending the embodiment of his weaknesses flying back into the seat. Turning his back to his other self, Shinji glared out the window.

{Why? Why you?}

"Because no one else can."

{You sound just like HIM! Why Do you even TRY to save that...that BASTARD KING of a father?!}

"Because, when I saw him in his office that day, I saw something I'd never noticed before. We had the same eyes."

{Of course you do! He provided one half of your genes!}

"No, I mean his eyes, they were like mine used to be, empty."

{So?! After all that he did to you, he deserves everything that happens to him!}

"I'm going to save him, and everybody else, I've already decided."

{You'll fail.}

Shinji turned to glare at his other self.

"No. I won't"

----------------------------Central Dogma------------------------------

Misato watched as the 1/1 Scale Balloon Dummy of Unit 01 was pulled into position by a small unmanned boat. She nodded to Lt. Hyuga, who input a few commands on his console. On screen, The Dummy raised its Pistol, only to be vaporized a moment later. To her left, Lt. Aoba reported on the status of this operation so far.

"The enemy's particle beam has hit, the Dummy has been vaporized!"

Not skipping a beat, Misato wrote some notes down on the clipboard she was holding, then turned back to the screen.

"Next!"

An automated train carrying a Model 12 Self Propelled Mortar took its position, the weapon targeting the Fifth Angel.

"The Mortar has locked on."

"Fire."

The mortar fired, its beam bouncing off of the Angel's A.T. Field. A moment later, the Angel retaliated with a beam of its own.

"The Model 12 Self Propelled Mortar has been destroyed!"

Misato smirked as the information she had gathered on the enemy all came together.

"I see."

Turning to her subordinates, Misato ordered Hyuga and Aoba to Analysis Room Two.

-------------------NERV Infirmary, Emergency Room-----------------------

Rei sat beside the machine that Shinji was hooked up to. She was confused, she did not know why she felt this way. Shinji had been hurt, hurt protecting her, even though she could be replaced. And it caused a pain in her heart, it made her feel cold, colder than she had ever felt. It was as if someone had taken a blanket soaked in freezing water and wrapped it around her. She stood up and walked to the machine's side, looking at the unconscious Third Children within. An almost inaudible gasp escaped Rei's lips, when a moment later, Shinji's eyes fluttered open. Seeing Rei standing there, he smiled beneath the transparent respirator mask.

----------------------------EVA Cage Seven------------------------------

Akagi Ritsuko watched as the melted pieces of armor plating on EVA-01 were methodically removed. The damage had been extensive and by her estimates if Shinji had been exposed to the beam for just three more minutes, he would have died.

"I don't get it."

"Get what Sempai?"

"Shinji. That boy could have died, pulling a maneuver like that."

"Hai. But, Unit 00 would not have survived a direct hit from the Angel. Rei would..."

"Would have died, I know, Maya."

Maya turned to face her senior, thinking for a moment how to word her next sentence.

"I thought it was kind of noble. He saved Rei's life. You don't see such selflessness anymore."

"Indeed you don't."

Ritsuko thought back to a few weeks ago, when Rei had been in her office for her routine examination.

[FLASHBACK]

'Oh _this_ just got interesting.'

When the First Children re-established eye contact with the scientist, Ritsuko could tell she was having trouble wording her thoughts.

"Shinji-kun's smile..."

'The Commander's son, huh?'

"...makes me feel warm."

"My,my...It appears our Rei has got herself a crush."

"A crush, Akagi-hakase?"

Ritsuko looked at the albino girl, realizing her attempt at teasing had failed, simply because Rei had no concept of what a crush was.

"A crush is a minor infatuation, due possibly to physical attraction or positive interactions with another individual."

Rei looked at Ritsuko blankly. The scientist sighed, realizing that the girl was now quite confused. Ritsuko knew that Rei wasn't stupid, but that she had very limited interaction with very few people.

"You like him, Rei."

"We are friends, are not friends supposed to "like" each other?"

"Its a bit different than that. But right now you shouldn't worry about it, just concentrate on the Unit 00 reactivation experiment."

"Hai, Akagi-hakase."

And without another word Rei turned and left.

[END FLASHBACK]

'You care for her, don't you, Shinji?'

-----------------------------Analysis Room Two--------------------------

"Alright, what do we know?"

Misato turned to Hyuga, whom began reading information off of his clipboard.

"From the data we've collected, we're assuming the target automatically attacks any opponent within a certain range. The likelihood of it hitting anything entering the area with its particle beam is 100%, too risky for close range combat in an EVA."

Misato nodded and then turned to Aoba.

"What about its A.T. Field?"

"It's still active. It's strong enough that the spatial changes in the phase are visible to the naked eye. Using half measures, such as guided missles, heavy artillery, or bombs will inflict more damage on us than the Angel."

"Hmm, offensively and defensively its almost perfect. A flying fortress. What's the status on that Drill?"

Hyuga cleared his throat and once again continued.

"At the moment the target is directly above us, penetrating the Tokyo-3 Null Zone. A giant shielded drill with a diameter of 17.5 meters is boring towards NERV would appear that the enemy is planning to attack NERV Headquarters directly."

"Sassy bastard. So what's its ETA?"

"12:06:54 AM. A little after midnight. By that time it will have breached all twenty two levels of armor, and arrive at NERV Headquarters itself."

Misato sighed.

'Less than ten hours, what can we do in that time?'

Misato was shaken from her thoughts by a report from the Central Dogma.

"The Drill has reached the first armor plate."

"What's the status on Unit 01?"

Ritsuko's voice now came through the communications system.

"The defensive armor was melted down to the third layer, the silver lining is that the central control unit sustained no damage. In three hours, the replacement parts should be installed."

"Understood, Unit 00?"

"Minor heat damage sustained on the hands, but otherwise undamaged. In all honesty, Rei would have been a sitting duck out there. There's still a feed back loop so actual combat-"

"-Is impossible."

While she felt guilty for truly almost getting Rei killed, Misato had to concentrate on formulating a plan to defeat the Angel.

"This situation sure isn't favorable."

Hyuga turned to the Ops Director.

"Should we raise the white flag?"

Misato thought for a moment, and then it hit her.

[FLASHBACK]

Shinji lifted the sniper rifle into position, taking aim at his target, and then firing. Misato watched as the target at the far end of the range took a direct hit to the head region. She clapped for a minute, alerting Shinji to her presence.

"I wouldn't have figured you the type for guns. That seems more of Aida-kun's cup of tea."

Shinji sighed and placed the rifle down.

"You never know when knowledge of things like this will come in handy."

[END FLASHBACK]

"Before we resort to that, there's one little thing I'd like to-"

Misato was cut off by her phone ringing. She looked at the phone and recognized Rei's number.

"Rei?"

"_Shinji-kun is conscious, and the medical staff is in the process of moving him._"

"Already?! Wow. Listen Rei, I need you on standby.

"_Understood, Captain Katsuragi._"

------------ NERV Commander's Office, Twenty Minutes Later----------

Sub-Commander Fuyutsuki was skeptical to say the least, thinking the plan that Ops Director had come up with seemed immpossible.

"You want a sniper to shoot the target from outside the Angel's firing zone?"

"Yes, Sir. Instead of trying to neutralize the targets A.T Field, I believe a pinpoint shot with a high energy beam is the only way."

"What do the MAGI say?"

"The response from the MAGI Super Computers were two affirmatives and one conditional affirmative."

"So our probability of success is 8.7 percent."

"It's quite a high percentage."

Gendou looked over his glasses at the captain. Her body language spoke of complete confidence in her plan, or was it in his son?

"I see no reason to raise an objection, you made proceed, Captain Katsuragi."

"Yes, sir"

-----------------------Several Hours Later------------------------------

"Fifty-six, Fifty-seven"

Sweat dripped on the floor from Shinji's forehead as he pushed himself up again, he had been doing one handed push-ups for a good while, alternating hands after each set of one hundred.

'"Strengthen the body as well as the mind." That's what Sensei said, in one of my first lessons.'

It had been sometime since Rei had left, saying that Misato had a plan to defeat the Angels. Shinji knew the plan, he just hoped it would still work, given that this angel, unlike the last two, had decided to adopt new tactics. It was actually quite frustrating when he stopped to think about it. He had been under the assumption that the Angels would attack the same way.

"Sixty-seven, sixty-eight."

In retrospect it had been kind of stupid to assume such. Angels weren't humans, they were infinitely more complex, so just because the people he knew didn't remember, that didn't mean the angels didn't. The first two angels could easily just not have shaken off the disorientation from the restart, an advantage that the Fifth Angel had. Like a stone tossed in the water, his actions thus far were creating a ripple effect. He would not be so presuming next time.

"Seventy-nine, Eighty."

The door hissed open, and Rei walked in wheeling a cart. Shinji assumed a sitting position and looked up at Rei.

"Misato-san has a plan, I take it?"

"Yes."

Rei reached into a pocket in her skirt and drew out a small, hand sized notebook.

"Pilots Ikari and Ayanami will arrive at the cage at 17:30 today. At 18:00 Unit 01 and Unit 00 will activate, launch is at 18:05. They will arrive at the temporary base on Futago-yama at 18:30, there they will stand by and await further orders. The operation begins promptly at midnight."

"Sounds good."

Rei reached under the cart and produced a new plugsuit, handing it to Shinji, who took it with a smile. Shinji looked to the tray on the cart, and picked up the carton of milk.

"Thanks for bringing me this, Rei-san"

"Y-yes."

Shinji downed the milk, after smiling at the albino girl's blushing, but let the other food sit, he never did have a liking to hospital rations.

"We'll be departing in sixty minutes."

"An hour, huh? I'll see you there, then."

---------------EVA Cage Seven, Thirty Minutes Later-------------

Shinji entered the cages, his plugsuit tucked under his arm. Looking across the hanger, he was his father talking to Rei.

'Wonder what they're talking about...'

After a minute or so of watching the exchange, Shinji turned to walk to his EVA, to begin his pre-launch checklist. A gruff voice stopped him however.

"Shinji."

The Third Children stopped and turned, shocked, to see his father standing a few feet away.

"Good luck, Shinji."

"Th-thank you, father."

--------------------Central Dogma, 18:00------------------------

"EVANGELION Unit 01 ready for launch."

"EVANGELION Unit 00 is also ready for launch."

"Roger. Moving EVAs to lift pads."

"Is the Commander there?"

"Yes, Pilot Ikari, he is."

"I won't fail, Father."

Gendou nodded slightly, not changing his expression.

"Carry on, pilot."

"Sir!"

----------------------Futago-yama, 18:30-------------------------

As Unit 01 and Unit 00 approached the site of the Operation, Shinji took note of all the equipment lacing the mountainside.

'I still wonder how Misato-san managed to get all this in place and hooked up in such a short while.'

As he arrived at the Field Base, Shinji brought Unit 01 into a crouch by the makeshift catwalk, and ejected the plug. After exiting his EVA and doing his best to dry the LCL off of his clothes, Shinji made his way to the command tent where Misato and Ritsuko stood, going over the last details of the Operation.

"Hey, Shinji-kun."

"Hey, Misato-san."

"You ready for this?"

"Heh, even if I'm not I have to do it anyway."

Misato looked at her ward for a moment, wording her thoughts.

"I'm sorry."

"Sorry? Sorry for what?"

"For getting you hurt."

Shinji smiled reassuringly.

"You did what you had to do as Director of Operations, no more no less. And while I may not have agreed with it, I don't think you should beat yourself up over it. I made the choice to throw myself in front of the Particle Beam."

Tears threatened to creep into Misato's eyes, but she staved them off, not wanting to show weakness in front of her subordinates. She did however allow herself a small smile.

"Fall in, pilot."

"Yes, Captain."

------------------------Futago-yama, 23:00-----------------------

"This operation is based around using the EVA Positron Sniper Rifle to deliver a precise shot to the angel's core. Here are your individual duties for this operation: Shinji-kun?

"Yes, ma'am?"

"Unit 01 will be the gunner."

"Understood."

"Rei, you're in charge of defense with Unit 00."

"Understood, Captain Katsuragi."

Ritsuko observed the two pilots for a moment; Shinji had a look of determination set in his features. She then added to Misato's orders.

"This is because of Shinji-kun's recent exercises with the sniper rifle, making him the most qualified for this position, as this operation will require exceptional precision. Since the positron beam will be influenced by Earth's gravity, magnetic fields and rotation, the beam will not fire in a straight line. You must remember to make adjustments for these deviations. You must penetrate the core precisely"

"Understood, this should be a piece of cake, Ma'am."

"Good to hear, just don't let that confidence cloud your aim."

"Right."

"Also, once you fire it, it will take time before you can fire again for cooling reloading and replacement of the fuses."

"So I have to try to take it out in one shot."

"Correct."

"It's time, both of you get changed."

"Yes, Ma'am."

------------------NERV Field HQ Makeshift Locker Room-------------------

Shinji finished pulling his plugsuit on, and pressurized it, before folding up his clothing and placing it on the bench beside him. He glanced at the First Children's shadow on the other side of the privacy curtain, forming his thoughts before putting words to them.

"Rei-san, can I ask you something?"

"What?"

"Why did you stay by me while I was out of it?"

"You chose to provide me with company while I was injured. I felt it was justified to provide you the same courtesy. Is that not what 'friends' do?"

Shinji chuckled a little, amused at the honesty of her response.

"Rei-san?"

"Yes?"

"I know you're in charge of defending me while I take the shot, but could you do me a favor? Don't die for me."

The request drew a small gasp out of the First Children. She turned to see Shinji's shadow exiting the tent. She pressurized her plugsuit and did the same. Soon they found themselves sitting on the makeshift catwalks leading to their EVAs. Rei glanced at Shinji who was looking up at the moon.

"Shinji-kun?"

"Yeah?"

"Why do you care so much about me?"

Shinji thought for a moment, phrasing his answer carefully.

"Because, Rei-san, you're a very special girl, don't forget that, even when others tell you different."

"I see."

Another few moments passed in silence

"It is time, Shinji-kun."

"I know."

Both pilots stood, and for a moment looked at each other.

"See you later, Rei-san."

The First Children nodded.

Both pilots walked to their entry plugs and proceeded to run through the activation routines. Once both EVANGELIONs were activated, they both moved into position; Unit 01 lying on its belly, and Unit 00 crouched a little distance away, and waited for the Operation to begin. All across Japan lights began to go out, their precious energy being siphoned to power the last hope against the Fifth Angel.

-------------------------Command Car------------------------------------

"The time is now 00:00:00."

"Commencing Operation Yashima."

Misato looked into the screen of the field equipment that had been installed in the vehicle.

"Shinji-kun, we're entrusting you with all the electricity of Japan. Good luck."

"Understood, and thanks, Misato-san"

Misato nodded and turned to her Field Techs.

"Initiate Primary connection."

"Initiating power transmission from districts number 1 through 803."

All around the mountain the equipment for the operation hummed to life, as the power began to build.

"All cooling systems, full power! Positron Charge is nominal."

"Initiate Secondary Connection!"

"All accelerators engaging."

"Activating convergence unit."

"Transmitting all power to Futago-yama temporary substation. No problems reported with tertiary connection."

"Release final Safety systems."

"Shinji-kun, clear the chamber!"

"Right, Hyuga-san."

---------------------EVANGELION SHOGOUKI--------------------------------

Shinji took a deep breath as the targeting computer decended into his line of sight. Down in the Command Car, the final adjustments were being made.

"Transmitting all energy to the Positron Rifle! 8...7...6...5..."

Seeing a spike in energy from the target, Maya whipped around to face Ritsuko and Misato.

"High Energy output is detected from the target!"

Ritsuko's head jerked towards her assistant.

"What did you say?!"

All while this was happening, Lt. Hyuga continued his countdown, and Shinji's targeting computer made its final calculations.

"...3...2...1!"

"Fire!"

Inside his EVA, Shinji did as ordered squeezing the trigger, and sending the positron beam surging forth. At the same time, Ramiel shifted configuration, Forming one long pyramid in front, with six smaller pyramids on either side. Energy coursed along all seven points, and as Shinji fired his Positron Rifle, Ramiel fired its Main beam, and began blasting the area with its six sub-points firing Positron Bursts with quick fire succession. This caught Shinji off guard enough that he almost forgot to dodge the first beam, but the force of the explosion behind him had tossed Unit 01 a few meters away. Around the Field HQ, vehicles and tents were flung around like toys in a child's tantrum. When the blasts stopped, Misato pulled herself to her feet, dreading that something had happened to the Third Children. On the screens, Unit 01 lay motionless.

"Shinji-kun! Shinji-kun! Are you alright?"

Silence.

"SHINJI-KUN!!"

And then Unit 01 began to drag itself.

"I'm...alright...beginning reload sequence..."

Hyuga returned to his instruments, beginning his end of the reload sequence. The reports from NERV HQ stated that the enemy had just penetrated the Geo-Front.

"Replacing fuses, initiating recharge! Barrel cooling in progress! Resuming Positron Charging"

The Angel returned to its original configuration, and began to pour its energy into its most powerful beam yet.

Shinji willed Unit 01 to its feet, hoisting the Positron rifle as it stood. Unit 01 raised the rifle to its shoulder, and stared down the barrel.

"Another high energy reading is emenating from the target!"

"Oh no!"

Shinji braced himself for the impact, only to see Rei throw Unit 00 in the beam's path.

"REI!"

The shield that Unit 00 was holding was beginning to melt away as the particle beam from the Fifth Angel continued to pour forth.

'She won't last a minute!'

"C'mon. COME ON!!"

"Shinji-kun, READY!!"

Shinji poured all of his concentration into this one shot. And three words escaped his lips as he pulled the trigger.

"I'll Kill You."

The beam surged forth with incredible velocity, punching through Ramiel's A.T. Field like it wasn't even there, and blasting through the angel, vaporizing its core on contact. As the Angel fell, cheers broke out in the Command Car.

"We Did IT!

Zerogouki collapsed onto its side, its armor melted. Shinji tossed the positron rifle down, the weapon landing with a hard crash. He rushed his EVA over to Unit 00, tearing off the shielding on the neck that housed the Entry plug. Pulling the plug out he watched as the heated LCL vented out. Bringing Unit 01 to a crouch and placing Unit 00's Entry Plug on the ground, Shinji ejected his own plug. Shinji climbed down his EVANGELION as fast as his legs would carry him, scrambling to Rei's Entry Plug. Ignoring the extreme heat burning his hands through his plug suit, Shinji forced the hatch open, tossing the hatch up and bolting inside.

"Rei-san! Rei-san! Are you alright?!"

The First Children looked up weakly at the Third Children. Shinji hurriedly embraced the albino girl, thankful that she was alive.

"Shinji-kun, is it Later yet?"

The question brought tears to Shinji's eyes and a smile to his lips.

"Yeah, Rei. It's Later."

* * *

**Next Episode-** The Fifth Angel lies dead, but because of the change in its attack strategy, Shinji is forced to rethink his entire plan. Realizing he can't do this alone, Shinji seeks out someone he beleives can help him, but wonders if he can trust him with such an important task.

Next Episode- **Shinrai**(Trust)

* * *

A/N- Sorry for this being so dry, at least its dry in my opinion, but I wanted to get inside some of the character's heads and see what they might be thinking after Shinji manages to get himself fried...again. I swear to you that the next one will be better. Also regarding what I would consider OOC-ness on the part of Gendou, this is a result of the comments that Shinji made in the last chapter. I can honestly say I'm not a Gendou Hater, I see him as a man who made the wrong choices. Hence why Shinji is attempting to save him. Keep in mind though that as Gendou is who he is that point will most likely take a good long time to come to fruition, and he will be in character for a good while to come. That being said I hope you enjoy the story thus far, and will join me for the next chapter when it comes out.


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